Title: Exploring Schoeneae GBS SNP data
Name: Tammy L. Elliott
Date: February 14, 2019
R version 3.5.1
Compare heterozygocity across different runs
This table shows the number of heterozygotes for three different runs with varying minimum depth of samples per loci. Row names represent specimen names.
## min.depth=4 min.depth=10 min.depth=20
## SchAre1 283 112 71
## SchAre2 232 115 67
## SchAur1 267 136 91
## SchAur2 341 173 108
## SchAuri1 717 398 125
## SchAuri2 120 84 68
## SchAuri3 306 68 41
## SchAuri4 66 44 34
## SchAuri5 84 58 36
## SchBol1 382 314 118
## SchBol2 93 61 49
## SchBol4 2946 1426 265
## SchCom1 792 531 138
## SchCom2 1445 690 206
## SchComp1 745 287 181
## SchComp2 1692 817 136
## SchCompA1 638 355 187
## SchCompA2 385 217 86
## SchCra1 532 249 119
## SchCras1 515 303 190
## SchCras2 2195 1158 176
## SchCusAur1 460 256 84
## SchCusAur2 1269 603 254
## SchCusB1 739 219 140
## SchCusB2 1535 784 244
## SchCusDn1 163 102 76
## SchCusDn2 1171 593 182
## SchCusDn3 4171 1215 469
## SchCusDr1 80 33 20
## SchCusDr2 2104 506 238
## SchCusDr3 536 133 63
## SchCusEC1 2957 682 218
## SchCusEC2 886 445 277
## SchCusEC3 164 91 65
## SchCusEF1 688 313 136
## SchCusJ1 648 291 175
## SchCusJ2 113 77 62
## SchCusJ3 898 479 227
## SchCusJ4 456 268 147
## SchCusJ5 251 169 148
## SchCusLG2 124 66 48
## SchCusP1 782 450 110
## SchCusP2 205 119 62
## SchEpi1 598 365 143
## SchEpi10 606 270 154
## SchEpi11 328 153 108
## SchEpi2 232 119 90
## SchEpi3 296 143 109
## SchEpi4 2306 671 163
## SchEpi5 305 160 91
## SchEpi6 510 206 141
## SchEpi7 370 145 94
## SchEpi8 466 233 174
## SchEpi9 1294 386 212
## SchExi1 106 56 37
## SchExi2 1354 735 155
## SchExi3 108 84 78
## SchExi4 715 323 202
## SchGra1 406 292 195
## SchGra2 410 251 189
## SchInc1 480 214 129
## SchLig1 2615 1200 307
## SchLim1 3650 655 269
## SchLim2 268 130 87
## SchLim3 96 45 37
## SchLor1 347 191 148
## SchLor2 4343 751 166
## SchMeg1 255 99 47
## SchNig1 631 178 99
## SchPic1 542 191 106
## SchPic2 232 135 88
## SchPic3 410 261 175
## SchPic4 303 169 97
## SchPse1 231 137 88
## SchPse2 502 256 158
## SchQua1 1145 672 278
## SchQua2 1526 434 184
## SchTri1 301 177 107
## SchTri2 313 216 158
## SchUnk 2562 1034 249Number of SNPs per sample
This table shows the number of SNPS per sample for three different runs with varying minimum depth of samples per loci. Row names represent specimen names.
## Sample min.depth=4 min.depth=10 min.depth=20
## 1 SchAre1 10043 5547 3548
## 2 SchAre2 7931 4180 2666
## 3 SchAur1 11990 6872 4609
## 4 SchAur2 11552 5714 3900
## 5 SchAuri1 15384 8476 3863
## 6 SchAuri2 6393 3904 2942
## 7 SchAuri3 6098 3184 2366
## 8 SchAuri4 3292 2510 1989
## 9 SchAuri5 4745 3209 2444
## 10 SchBol1 11797 7069 3755
## 11 SchBol2 3890 2657 1970
## 12 SchBol4 27888 10901 4166
## 13 SchCom1 16832 10497 4404
## 14 SchCom2 24685 11223 4219
## 15 SchComp1 15690 8628 5529
## 16 SchComp2 20510 11069 5286
## 17 SchCompA1 16847 9434 4971
## 18 SchCompA2 10841 7128 3930
## 19 SchCra1 13125 6167 4040
## 20 SchCras1 19477 10557 6201
## 21 SchCras2 26558 12816 5365
## 22 SchCusAur1 13842 7406 3129
## 23 SchCusAur2 22946 11918 5801
## 24 SchCusB1 15349 8336 5141
## 25 SchCusB2 26235 12595 5522
## 26 SchCusDn1 5148 3276 2441
## 27 SchCusDn2 18445 8218 3664
## 28 SchCusDn3 42757 15491 7352
## 29 SchCusDr1 4518 2424 1720
## 30 SchCusDr2 24396 10474 5982
## 31 SchCusDr3 9176 3478 1789
## 32 SchCusEC1 32858 11846 5898
## 33 SchCusEC2 18701 8786 5608
## 34 SchCusEC3 6357 3075 2205
## 35 SchCusEF1 17020 7577 4064
## 36 SchCusJ1 15178 7723 4849
## 37 SchCusJ2 6637 4334 2799
## 38 SchCusJ3 21735 11124 5739
## 39 SchCusJ4 12285 7420 4586
## 40 SchCusJ5 6053 3745 2824
## 41 SchCusLG2 5033 3261 2451
## 42 SchCusP1 16401 9888 5224
## 43 SchCusP2 10295 5513 3303
## 44 SchEpi1 15623 9505 5384
## 45 SchEpi10 13205 7369 4915
## 46 SchEpi11 8671 6243 5062
## 47 SchEpi2 9082 5203 3973
## 48 SchEpi3 10863 6063 4362
## 49 SchEpi4 22677 8237 3768
## 50 SchEpi5 10377 6745 5145
## 51 SchEpi6 12247 6519 4727
## 52 SchEpi7 15936 7291 4913
## 53 SchEpi8 13229 6955 4818
## 54 SchEpi9 19315 8609 5693
## 55 SchExi1 3696 2874 2269
## 56 SchExi2 19283 10293 3733
## 57 SchExi3 3829 2834 2291
## 58 SchExi4 16512 8171 5431
## 59 SchGra1 13052 8473 6033
## 60 SchGra2 9628 6656 5063
## 61 SchInc1 11386 6116 4515
## 62 SchLig1 29151 13024 5163
## 63 SchLim1 31721 10445 6044
## 64 SchLim2 8335 4487 3267
## 65 SchLim3 4065 2940 2222
## 66 SchLor1 11851 7232 5221
## 67 SchLor2 36665 9507 4678
## 68 SchMeg1 8539 5006 3233
## 69 SchNig1 11376 5929 4440
## 70 SchPic1 11621 6362 3695
## 71 SchPic2 7850 5490 4235
## 72 SchPic3 11974 7586 5477
## 73 SchPic4 9853 5925 4015
## 74 SchPse1 10611 7041 5151
## 75 SchPse2 13295 7919 5609
## 76 SchQua1 25141 11815 6279
## 77 SchQua2 23518 9740 5134
## 78 SchTri1 10166 6742 4350
## 79 SchTri2 8767 6621 5231
## 80 SchUnk 30361 12737 4939Mean depth SNPs per sample
This table shows the mean depth of SNPS per sample for three different runs with varying minimum depth of samples per loci. Row names represent specimen names.
## Sample min.depth=4 min.depth=10 min.depth=20
## 1 SchAre1 332.63298 250.63 155.58
## 2 SchAre2 259.11650 190.49 156.86
## 3 SchAur1 270.22961 204.64 132.12
## 4 SchAur2 194.61357 184.96 124.45
## 5 SchAuri1 114.88989 132.40 135.09
## 6 SchAuri2 174.47286 164.64 147.16
## 7 SchAuri3 157.81732 152.59 109.83
## 8 SchAuri4 117.12819 117.99 131.49
## 9 SchAuri5 117.07524 125.87 131.02
## 10 SchBol1 117.72323 129.82 140.72
## 11 SchBol2 95.76761 109.98 119.54
## 12 SchBol4 143.74351 190.85 194.29
## 13 SchCom1 183.18518 184.51 223.23
## 14 SchCom2 147.49508 172.84 170.28
## 15 SchComp1 289.17304 283.98 215.20
## 16 SchComp2 254.08108 235.54 198.76
## 17 SchCompA1 177.73253 144.67 120.93
## 18 SchCompA2 169.43548 123.35 121.72
## 19 SchCra1 327.40830 374.74 271.23
## 20 SchCras1 226.86605 229.01 268.39
## 21 SchCras2 195.60110 235.75 193.39
## 22 SchCusAur1 87.12715 102.41 122.71
## 23 SchCusAur2 184.77652 181.15 189.55
## 24 SchCusB1 217.61783 219.17 214.08
## 25 SchCusB2 164.04010 199.98 185.91
## 26 SchCusDn1 128.74456 136.06 137.86
## 27 SchCusDn2 117.90583 148.31 152.37
## 28 SchCusDn3 353.84279 486.21 382.98
## 29 SchCusDr1 89.27202 86.15 88.14
## 30 SchCusDr2 267.03082 314.35 308.58
## 31 SchCusDr3 97.37947 119.09 128.31
## 32 SchCusEC1 223.28766 258.37 297.46
## 33 SchCusEC2 355.05572 330.13 307.13
## 34 SchCusEC3 96.65345 117.54 110.66
## 35 SchCusEF1 170.94835 211.04 225.80
## 36 SchCusJ1 236.28963 255.50 187.95
## 37 SchCusJ2 95.58490 89.30 91.77
## 38 SchCusJ3 201.91199 240.48 250.44
## 39 SchCusJ4 268.86561 288.88 299.65
## 40 SchCusJ5 132.80704 133.27 140.66
## 41 SchCusLG2 92.32446 97.93 110.86
## 42 SchCusP1 217.65472 219.43 239.69
## 43 SchCusP2 87.54182 99.54 95.36
## 44 SchEpi1 125.66613 114.99 118.82
## 45 SchEpi10 298.50201 241.55 220.85
## 46 SchEpi11 125.31219 118.95 124.05
## 47 SchEpi2 176.50132 147.85 135.30
## 48 SchEpi3 112.10467 115.16 110.16
## 49 SchEpi4 115.88160 122.66 113.08
## 50 SchEpi5 253.49253 168.17 142.10
## 51 SchEpi6 249.01837 188.79 160.97
## 52 SchEpi7 589.43367 174.16 140.75
## 53 SchEpi8 160.08058 138.60 114.67
## 54 SchEpi9 243.31442 220.57 194.90
## 55 SchExi1 167.22673 128.51 117.85
## 56 SchExi2 132.94104 154.28 168.88
## 57 SchExi3 130.93314 147.60 161.59
## 58 SchExi4 281.84314 343.49 275.46
## 59 SchGra1 258.14350 228.82 219.69
## 60 SchGra2 174.97798 144.25 140.48
## 61 SchInc1 187.73301 164.69 151.10
## 62 SchLig1 161.61535 176.72 179.22
## 63 SchLim1 316.70417 349.34 246.84
## 64 SchLim2 138.97457 145.22 121.53
## 65 SchLim3 137.12251 132.91 111.70
## 66 SchLor1 193.19247 216.54 196.22
## 67 SchLor2 329.15871 321.90 221.20
## 68 SchMeg1 228.74294 174.87 108.43
## 69 SchNig1 92.37825 94.90 102.49
## 70 SchPic1 534.24963 457.96 296.17
## 71 SchPic2 188.43185 157.77 132.84
## 72 SchPic3 318.22749 264.42 219.92
## 73 SchPic4 324.00010 225.30 161.86
## 74 SchPse1 162.49967 133.79 108.10
## 75 SchPse2 339.60647 274.79 175.24
## 76 SchQua1 184.33332 203.65 187.19
## 77 SchQua2 207.79905 284.26 314.53
## 78 SchTri1 197.87675 154.16 118.68
## 79 SchTri2 225.27216 170.07 148.82
## 80 SchUnk 191.62709 269.79 265.21Barplots showing number of SNPs per loci across three different minimum depth per sampling runs
Inspect minimum sampling depth per locus = 4 in more detail:
Show taxa below 7000 SNPS
## Sample freq
## 6 SchAuri2 6393
## 7 SchAuri3 6098
## 8 SchAuri4 3292
## 9 SchAuri5 4745
## 11 SchBol2 3890
## 26 SchCusDn1 5148
## 29 SchCusDr1 4518
## 34 SchCusEC3 6357
## 37 SchCusJ2 6637
## 40 SchCusJ5 6053
## 41 SchCusLG2 5033
## 55 SchExi1 3696
## 57 SchExi3 3829
## 65 SchLim3 4065Inspect minimum sampling depth per locus = 10 in more detail:
Show taxa below 3500 SNPS
## Sample freq
## 7 SchAuri3 3184
## 8 SchAuri4 2510
## 9 SchAuri5 3209
## 11 SchBol2 2657
## 26 SchCusDn1 3276
## 29 SchCusDr1 2424
## 31 SchCusDr3 3478
## 34 SchCusEC3 3075
## 41 SchCusLG2 3261
## 55 SchExi1 2874
## 57 SchExi3 2834
## 65 SchLim3 2940Inspect minimum sampling depth per locus = 20 in more detail:
Show taxa below 2500 SNPS
## Sample freq
## 7 SchAuri3 2366
## 8 SchAuri4 1989
## 9 SchAuri5 2444
## 11 SchBol2 1970
## 26 SchCusDn1 2441
## 29 SchCusDr1 1720
## 31 SchCusDr3 1789
## 34 SchCusEC3 2205
## 41 SchCusLG2 2451
## 55 SchExi1 2269
## 57 SchExi3 2291
## 65 SchLim3 2222Show difference in taxa between three analyses
# Difference between mindepth 4 and 10
(low.SNPS.diff.4.10<-setdiff(saschoenus.SNPS.mindepth4.few.loci$Sample, saschoenus.SNPS.mindepth10.few.loci$Sample))## [1] "SchAuri2" "SchCusJ2" "SchCusJ5"#Difference between mindepth 4 and 20
(low.SNPS.diff.4.20<-setdiff(saschoenus.SNPS.mindepth4.few.loci$Sample, saschoenus.SNPS.mindepth20.few.loci$Sample))## [1] "SchAuri2" "SchCusJ2" "SchCusJ5"#Difference between mindepth 10 and 20
(low.SNPS.diff.10.20<-setdiff(saschoenus.SNPS.mindepth10.few.loci$Sample, saschoenus.SNPS.mindepth20.few.loci$Sample))## character(0)Tammy’s comments
I have decided that the following samples are to be dropped because of relatively low number of SNPS: SchAuri3, SchAuri4, SchAuri5, SchBol2, SchCusDn1, SchCusDr1, SchCusDr3, SchCusEC3, SchCusLG2, SchExi1, SchExi3, SchLim3 <>
I have decided not to drop the following three specimens, as they are above the cut-offs for both the minimum depth 10 and 20 runs, and only slightly below the cut-off for the minimum sample depth of 4 run: SchAuri2, SchCusJ2, SchCusJ5 <>
Violin plots summarizing coverage per specimen
Violin plots for minimum depth of four samples per loci
Violin plots for minimum depth of ten samples per loci
Violin plots for minimum depth of twenty samples per loci
Counts by level of homozygosity and heterozygosity for each specimen
## $SchAre1
## x freq
## 1 0/0 8081
## 2 0/1 138
## 3 0/2 6
## 4 1/0 132
## 5 1/1 1607
## 6 1/2 3
## 7 2/0 1
## 8 2/1 2
## 9 2/2 51
## 10 3/0 1
## 11 3/3 1
## 12 <NA> 127387
##
## $SchAre2
## x freq
## 1 0/0 6482
## 2 0/1 121
## 3 0/2 2
## 4 1/0 103
## 5 1/1 1183
## 6 2/0 6
## 7 2/2 28
## 8 3/3 1
## 9 <NA> 129484
##
## $SchAur1
## x freq
## 1 0/0 10179
## 2 0/1 152
## 3 0/2 5
## 4 1/0 101
## 5 1/1 1480
## 6 2/0 7
## 7 2/1 2
## 8 2/2 39
## 9 3/3 3
## 10 <NA> 125442
##
## $SchAur2
## x freq
## 1 0/0 9552
## 2 0/1 186
## 3 0/2 2
## 4 1/0 142
## 5 1/1 1557
## 6 1/2 1
## 7 2/0 6
## 8 2/1 4
## 9 2/2 63
## 10 3/3 4
## 11 <NA> 125893
##
## $SchAuri1
## x freq
## 1 0/0 12807
## 2 0/1 357
## 3 0/2 14
## 4 1/0 336
## 5 1/1 1787
## 6 1/2 1
## 7 2/0 8
## 8 2/1 1
## 9 2/2 47
## 10 3/3 3
## 11 <NA> 122049
##
## $SchAuri2
## x freq
## 1 0/0 5396
## 2 0/1 67
## 3 1/0 50
## 4 1/1 835
## 5 1/2 1
## 6 2/0 2
## 7 2/2 21
## 8 3/3 2
## 9 <NA> 131036
##
## $SchAuri3
## x freq
## 1 0/0 5098
## 2 0/1 140
## 3 0/2 2
## 4 1/0 161
## 5 1/1 659
## 6 2/0 2
## 7 2/1 1
## 8 2/2 19
## 9 3/3 1
## 10 <NA> 131327
##
## $SchAuri4
## x freq
## 1 0/0 2975
## 2 0/1 44
## 3 1/0 21
## 4 1/1 245
## 5 2/0 1
## 6 2/2 4
## 7 <NA> 134120
##
## $SchAuri5
## x freq
## 1 0/0 4198
## 2 0/1 58
## 3 0/2 1
## 4 1/0 24
## 5 1/1 445
## 6 2/1 1
## 7 2/2 14
## 8 <NA> 132669
##
## $SchBol1
## x freq
## 1 0/0 10093
## 2 0/1 188
## 3 0/2 8
## 4 1/0 183
## 5 1/1 1265
## 6 2/0 3
## 7 2/2 37
## 8 3/3 1
## 9 <NA> 125632
##
## $SchBol2
## x freq
## 1 0/0 3458
## 2 0/1 49
## 3 1/0 43
## 4 1/1 323
## 5 2/0 1
## 6 2/2 6
## 7 3/3 1
## 8 <NA> 133529
##
## $SchBol4
## x freq
## 1 0/0 21273
## 2 0/1 1453
## 3 0/2 25
## 4 1/0 1415
## 5 1/1 3540
## 6 1/2 10
## 7 2/0 33
## 8 2/1 10
## 9 2/2 95
## 10 3/3 4
## 11 <NA> 109552
##
## $SchCom1
## x freq
## 1 0/0 14164
## 2 0/1 413
## 3 0/2 10
## 4 0/3 1
## 5 1/0 350
## 6 1/1 1784
## 7 1/2 5
## 8 2/0 10
## 9 2/1 3
## 10 2/2 44
## 11 3/3 3
## 12 <NA> 120623
##
## $SchCom2
## x freq
## 1 0/0 20393
## 2 0/1 695
## 3 0/2 18
## 4 1/0 697
## 5 1/1 2765
## 6 1/2 7
## 7 2/0 20
## 8 2/1 7
## 9 2/2 51
## 10 3/0 1
## 11 3/3 1
## 12 <NA> 112755
##
## $SchComp1
## x freq
## 1 0/0 12891
## 2 0/1 333
## 3 0/2 11
## 4 1/0 381
## 5 1/1 1990
## 6 1/2 4
## 7 1/3 1
## 8 2/0 12
## 9 2/1 3
## 10 2/2 35
## 11 3/3 2
## 12 <NA> 121747
##
## $SchComp2
## x freq
## 1 0/0 16431
## 2 0/1 808
## 3 0/2 18
## 4 0/3 1
## 5 1/0 826
## 6 1/1 2284
## 7 1/2 3
## 8 2/0 30
## 9 2/1 6
## 10 2/2 70
## 11 3/3 2
## 12 <NA> 116931
##
## $SchCompA1
## x freq
## 1 0/0 13981
## 2 0/1 309
## 3 0/2 6
## 4 1/0 313
## 5 1/1 2148
## 6 1/2 1
## 7 2/0 5
## 8 2/1 3
## 9 2/2 56
## 10 2/3 1
## 11 <NA> 120587
##
## $SchCompA2
## x freq
## 1 0/0 9347
## 2 0/1 197
## 3 0/2 3
## 4 1/0 180
## 5 1/1 1045
## 6 2/0 4
## 7 2/1 1
## 8 2/2 39
## 9 <NA> 126594
##
## $SchCra1
## x freq
## 1 0/0 10778
## 2 0/1 246
## 3 0/2 5
## 4 1/0 264
## 5 1/1 1726
## 6 1/2 2
## 7 2/0 11
## 8 2/1 3
## 9 2/2 60
## 10 3/0 1
## 11 3/3 3
## 12 <NA> 124311
##
## $SchCras1
## x freq
## 1 0/0 16464
## 2 0/1 256
## 3 0/2 9
## 4 1/0 242
## 5 1/1 2401
## 6 1/2 1
## 7 2/0 4
## 8 2/1 2
## 9 2/2 79
## 10 3/2 1
## 11 <NA> 117951
##
## $SchCras2
## x freq
## 1 0/0 21521
## 2 0/1 1088
## 3 0/2 23
## 4 0/3 1
## 5 1/0 1051
## 6 1/1 2745
## 7 1/2 2
## 8 2/0 25
## 9 2/1 5
## 10 2/2 68
## 11 <NA> 110881
##
## $SchCusAur1
## x freq
## 1 0/0 11628
## 2 0/1 227
## 3 0/2 9
## 4 1/0 208
## 5 1/1 1703
## 6 1/2 6
## 7 2/0 7
## 8 2/1 3
## 9 2/2 47
## 10 3/3 1
## 11 <NA> 123571
##
## $SchCusAur2
## x freq
## 1 0/0 19239
## 2 0/1 671
## 3 0/2 17
## 4 0/3 1
## 5 1/0 554
## 6 1/1 2334
## 7 1/2 3
## 8 2/0 20
## 9 2/1 3
## 10 2/2 68
## 11 3/3 1
## 12 <NA> 114499
##
## $SchCusB1
## x freq
## 1 0/0 12732
## 2 0/1 365
## 3 0/2 7
## 4 1/0 349
## 5 1/1 1799
## 6 1/2 3
## 7 2/0 8
## 8 2/1 5
## 9 2/2 55
## 10 3/0 2
## 11 3/3 2
## 12 <NA> 122083
##
## $SchCusB2
## x freq
## 1 0/0 21823
## 2 0/1 746
## 3 0/2 19
## 4 0/3 1
## 5 1/0 738
## 6 1/1 2758
## 7 1/2 2
## 8 2/0 25
## 9 2/1 4
## 10 2/2 67
## 11 3/3 5
## 12 <NA> 111222
##
## $SchCusDn1
## x freq
## 1 0/0 4502
## 2 0/1 88
## 3 1/0 75
## 4 1/1 463
## 5 2/2 13
## 6 <NA> 132269
##
## $SchCusDn2
## x freq
## 1 0/0 14974
## 2 0/1 536
## 3 0/2 18
## 4 1/0 596
## 5 1/1 2238
## 6 1/2 5
## 7 2/0 13
## 8 2/1 3
## 9 2/2 49
## 10 3/3 1
## 11 <NA> 118977
##
## $SchCusDn3
## x freq
## 1 0/0 32215
## 2 0/1 2017
## 3 0/2 37
## 4 0/3 2
## 5 1/0 2019
## 6 1/1 6132
## 7 1/2 18
## 8 2/0 60
## 9 2/1 14
## 10 2/2 183
## 11 3/0 2
## 12 3/1 2
## 13 3/3 6
## 14 <NA> 94703
##
## $SchCusDr1
## x freq
## 1 0/0 3816
## 2 0/1 49
## 3 1/0 30
## 4 1/1 604
## 5 2/0 1
## 6 2/2 13
## 7 <NA> 132897
##
## $SchCusDr2
## x freq
## 1 0/0 18915
## 2 0/1 1009
## 3 0/2 18
## 4 0/3 1
## 5 1/0 1037
## 6 1/1 3226
## 7 1/2 10
## 8 2/0 22
## 9 2/1 7
## 10 2/2 101
## 11 3/3 2
## 12 <NA> 113062
##
## $SchCusDr3
## x freq
## 1 0/0 7071
## 2 0/1 257
## 3 0/2 1
## 4 1/0 269
## 5 1/1 1528
## 6 1/2 2
## 7 2/0 6
## 8 2/1 1
## 9 2/2 37
## 10 3/3 1
## 11 <NA> 128237
##
## $SchCusEC1
## x freq
## 1 0/0 24910
## 2 0/1 1431
## 3 0/2 46
## 4 1/0 1412
## 5 1/1 4791
## 6 1/2 12
## 7 2/0 40
## 8 2/1 14
## 9 2/2 119
## 10 3/0 1
## 11 3/2 1
## 12 3/3 1
## 13 <NA> 104632
##
## $SchCusEC2
## x freq
## 1 0/0 15415
## 2 0/1 426
## 3 0/2 13
## 4 1/0 422
## 5 1/1 2311
## 6 1/2 3
## 7 2/0 17
## 8 2/1 4
## 9 2/2 50
## 10 3/1 1
## 11 3/3 3
## 12 <NA> 118745
##
## $SchCusEC3
## x freq
## 1 0/0 5266
## 2 0/1 84
## 3 0/2 2
## 4 1/0 75
## 5 1/1 878
## 6 1/2 1
## 7 2/0 2
## 8 2/2 35
## 9 <NA> 131067
##
## $SchCusEF1
## x freq
## 1 0/0 14270
## 2 0/1 340
## 3 0/2 14
## 4 1/0 320
## 5 1/1 1963
## 6 1/2 1
## 7 2/0 9
## 8 2/1 2
## 9 2/2 64
## 10 2/3 1
## 11 3/0 1
## 12 3/3 1
## 13 <NA> 120424
##
## $SchCusJ1
## x freq
## 1 0/0 12355
## 2 0/1 321
## 3 0/2 10
## 4 1/0 297
## 5 1/1 2065
## 6 1/2 3
## 7 2/0 13
## 8 2/1 4
## 9 2/2 69
## 10 3/3 3
## 11 <NA> 122270
##
## $SchCusJ2
## x freq
## 1 0/0 5790
## 2 0/1 53
## 3 0/2 2
## 4 1/0 58
## 5 1/1 712
## 6 2/2 19
## 7 <NA> 130776
##
## $SchCusJ3
## x freq
## 1 0/0 18004
## 2 0/1 434
## 3 0/2 12
## 4 1/0 432
## 5 1/1 2728
## 6 1/2 6
## 7 2/0 9
## 8 2/1 5
## 9 2/2 72
## 10 3/3 2
## 11 <NA> 115706
##
## $SchCusJ4
## x freq
## 1 0/0 10563
## 2 0/1 240
## 3 0/2 4
## 4 1/0 203
## 5 1/1 1197
## 6 1/2 1
## 7 2/0 6
## 8 2/1 2
## 9 2/2 25
## 10 3/3 2
## 11 <NA> 125167
##
## $SchCusJ5
## x freq
## 1 0/0 5117
## 2 0/1 129
## 3 0/2 1
## 4 1/0 120
## 5 1/1 659
## 6 2/2 18
## 7 3/0 1
## 8 3/3 1
## 9 <NA> 131364
##
## $SchCusLG2
## x freq
## 1 0/0 4473
## 2 0/1 71
## 3 0/2 2
## 4 1/0 48
## 5 1/1 408
## 6 1/2 2
## 7 2/0 1
## 8 2/2 18
## 9 <NA> 132387
##
## $SchCusP1
## x freq
## 1 0/0 13985
## 2 0/1 418
## 3 0/2 3
## 4 1/0 338
## 5 1/1 1553
## 6 2/0 16
## 7 2/1 7
## 8 2/2 53
## 9 3/3 2
## 10 <NA> 121035
##
## $SchCusP2
## x freq
## 1 0/0 8873
## 2 0/1 91
## 3 0/2 1
## 4 1/0 107
## 5 1/1 1178
## 6 1/2 2
## 7 2/0 4
## 8 2/2 26
## 9 3/3 1
## 10 <NA> 127127
##
## $SchEpi1
## x freq
## 1 0/0 13436
## 2 0/1 305
## 3 0/2 5
## 4 1/0 278
## 5 1/1 1522
## 6 1/2 1
## 7 2/0 5
## 8 2/1 4
## 9 2/2 50
## 10 3/3 2
## 11 <NA> 121802
##
## $SchEpi10
## x freq
## 1 0/0 10942
## 2 0/1 315
## 3 0/2 4
## 4 1/0 274
## 5 1/1 1591
## 6 1/2 3
## 7 2/0 6
## 8 2/1 3
## 9 2/2 50
## 10 3/1 1
## 11 <NA> 124221
##
## $SchEpi11
## x freq
## 1 0/0 7581
## 2 0/1 154
## 3 0/2 6
## 4 1/0 164
## 5 1/1 723
## 6 2/0 3
## 7 2/2 27
## 8 3/2 1
## 9 3/3 1
## 10 <NA> 128750
##
## $SchEpi2
## x freq
## 1 0/0 7747
## 2 0/1 111
## 3 0/2 3
## 4 1/0 114
## 5 1/1 1051
## 6 1/2 1
## 7 2/0 2
## 8 2/1 1
## 9 2/2 29
## 10 3/3 1
## 11 <NA> 128350
##
## $SchEpi3
## x freq
## 1 0/0 9060
## 2 0/1 152
## 3 0/2 3
## 4 1/0 135
## 5 1/1 1436
## 6 2/0 4
## 7 2/1 1
## 8 2/2 53
## 9 3/0 1
## 10 3/3 3
## 11 <NA> 126562
##
## $SchEpi4
## x freq
## 1 0/0 16143
## 2 0/1 1162
## 3 0/2 37
## 4 1/0 1049
## 5 1/1 4091
## 6 1/2 14
## 7 2/0 25
## 8 2/1 18
## 9 2/2 109
## 10 3/0 1
## 11 3/3 3
## 12 <NA> 114758
##
## $SchEpi5
## x freq
## 1 0/0 8801
## 2 0/1 165
## 3 0/2 4
## 4 1/0 132
## 5 1/1 1210
## 6 2/0 2
## 7 2/1 2
## 8 2/2 38
## 9 3/3 2
## 10 <NA> 127054
##
## $SchEpi6
## x freq
## 1 0/0 9945
## 2 0/1 247
## 3 0/2 6
## 4 1/0 245
## 5 1/1 1705
## 6 1/2 2
## 7 2/0 9
## 8 2/1 1
## 9 2/2 70
## 10 <NA> 125180
##
## $SchEpi7
## x freq
## 1 0/0 12889
## 2 0/1 195
## 3 0/2 2
## 4 1/0 162
## 5 1/1 2590
## 6 1/2 1
## 7 2/0 8
## 8 2/1 2
## 9 2/2 59
## 10 3/3 3
## 11 <NA> 121499
##
## $SchEpi8
## x freq
## 1 0/0 11178
## 2 0/1 236
## 3 0/2 2
## 4 1/0 222
## 5 1/1 1526
## 6 1/2 1
## 7 2/0 4
## 8 2/1 1
## 9 2/2 35
## 10 3/3 1
## 11 <NA> 124204
##
## $SchEpi9
## x freq
## 1 0/0 14964
## 2 0/1 622
## 3 0/2 18
## 4 1/0 620
## 5 1/1 2952
## 6 1/2 7
## 7 2/0 15
## 8 2/1 12
## 9 2/2 75
## 10 3/3 2
## 11 <NA> 118123
##
## $SchExi1
## x freq
## 1 0/0 3163
## 2 0/1 56
## 3 0/2 3
## 4 1/0 44
## 5 1/1 406
## 6 1/2 2
## 7 2/0 1
## 8 2/2 10
## 9 <NA> 133725
##
## $SchExi2
## x freq
## 1 0/0 15747
## 2 0/1 659
## 3 0/2 21
## 4 1/0 646
## 5 1/1 2099
## 6 1/2 3
## 7 2/0 21
## 8 2/1 4
## 9 2/2 55
## 10 3/3 2
## 11 <NA> 118153
##
## $SchExi3
## x freq
## 1 0/0 3419
## 2 0/1 57
## 3 1/0 49
## 4 1/1 283
## 5 2/0 1
## 6 2/1 1
## 7 2/2 15
## 8 <NA> 133585
##
## $SchExi4
## x freq
## 1 0/0 13740
## 2 0/1 342
## 3 0/2 10
## 4 0/3 1
## 5 1/0 349
## 6 1/1 1953
## 7 1/2 2
## 8 2/0 8
## 9 2/1 2
## 10 2/2 62
## 11 3/0 1
## 12 3/3 2
## 13 <NA> 120938
##
## $SchGra1
## x freq
## 1 0/0 11100
## 2 0/1 226
## 3 0/2 1
## 4 0/3 1
## 5 1/0 172
## 6 1/1 1483
## 7 1/2 1
## 8 2/0 4
## 9 2/1 1
## 10 2/2 37
## 11 3/3 3
## 12 <NA> 124381
##
## $SchGra2
## x freq
## 1 0/0 8079
## 2 0/1 217
## 3 0/2 2
## 4 1/0 185
## 5 1/1 1100
## 6 1/2 1
## 7 2/0 5
## 8 2/2 23
## 9 3/3 2
## 10 <NA> 127796
##
## $SchInc1
## x freq
## 1 0/0 9244
## 2 0/1 219
## 3 0/2 4
## 4 0/3 1
## 5 1/0 241
## 6 1/1 1568
## 7 1/2 3
## 8 1/3 2
## 9 2/0 7
## 10 2/1 2
## 11 2/2 69
## 12 3/0 1
## 13 3/3 2
## 14 <NA> 126047
##
## $SchLig1
## x freq
## 1 0/0 23308
## 2 0/1 1290
## 3 0/2 25
## 4 0/3 1
## 5 1/0 1259
## 6 1/1 3121
## 7 1/2 6
## 8 2/0 26
## 9 2/1 8
## 10 2/2 83
## 11 3/3 2
## 12 <NA> 108281
##
## $SchLim1
## x freq
## 1 0/0 22588
## 2 0/1 1721
## 3 0/2 42
## 4 0/3 1
## 5 1/0 1778
## 6 1/1 5267
## 7 1/2 19
## 8 2/0 57
## 9 2/1 29
## 10 2/2 155
## 11 3/0 2
## 12 3/1 1
## 13 3/3 4
## 14 <NA> 105746
##
## $SchLim2
## x freq
## 1 0/0 6878
## 2 0/1 133
## 3 0/2 4
## 4 1/0 130
## 5 1/1 1151
## 6 2/0 1
## 7 2/2 31
## 8 3/3 2
## 9 <NA> 129080
##
## $SchLim3
## x freq
## 1 0/0 3700
## 2 0/1 55
## 3 1/0 38
## 4 1/1 261
## 5 2/0 3
## 6 2/2 5
## 7 <NA> 133348
##
## $SchLor1
## x freq
## 1 0/0 10283
## 2 0/1 179
## 3 0/2 3
## 4 1/0 162
## 5 1/1 1158
## 6 2/0 2
## 7 2/1 1
## 8 2/2 35
## 9 3/3 1
## 10 <NA> 125586
##
## $SchLor2
## x freq
## 1 0/0 27009
## 2 0/1 2075
## 3 0/2 33
## 4 0/3 1
## 5 1/0 2150
## 6 1/1 5118
## 7 1/2 19
## 8 2/0 53
## 9 2/1 11
## 10 2/2 139
## 11 3/0 1
## 12 3/3 3
## 13 <NA> 100798
##
## $SchMeg1
## x freq
## 1 0/0 7157
## 2 0/1 121
## 3 0/2 5
## 4 1/0 128
## 5 1/1 1081
## 6 2/0 1
## 7 2/2 33
## 8 3/3 1
## 9 <NA> 128883
##
## $SchNig1
## x freq
## 1 0/0 9017
## 2 0/1 308
## 3 0/2 9
## 4 1/0 294
## 5 1/1 1653
## 6 1/2 4
## 7 2/0 12
## 8 2/1 4
## 9 2/2 65
## 10 3/3 2
## 11 <NA> 126042
##
## $SchPic1
## x freq
## 1 0/0 9421
## 2 0/1 275
## 3 0/2 12
## 4 1/0 246
## 5 1/1 1594
## 6 1/2 3
## 7 2/0 3
## 8 2/1 3
## 9 2/2 42
## 10 <NA> 125811
##
## $SchPic2
## x freq
## 1 0/0 6880
## 2 0/1 108
## 3 0/2 4
## 4 1/0 116
## 5 1/1 707
## 6 2/0 3
## 7 2/1 1
## 8 2/2 14
## 9 3/3 2
## 10 <NA> 129575
##
## $SchPic3
## x freq
## 1 0/0 10173
## 2 0/1 207
## 3 0/2 4
## 4 1/0 192
## 5 1/1 1324
## 6 1/3 1
## 7 2/0 4
## 8 2/1 2
## 9 2/2 38
## 10 3/3 1
## 11 <NA> 125464
##
## $SchPic4
## x freq
## 1 0/0 8158
## 2 0/1 167
## 3 0/2 5
## 4 1/0 127
## 5 1/1 1340
## 6 1/2 1
## 7 2/0 3
## 8 2/2 29
## 9 3/3 1
## 10 <NA> 127579
##
## $SchPse1
## x freq
## 1 0/0 9329
## 2 0/1 131
## 3 0/2 1
## 4 1/0 95
## 5 1/1 1008
## 6 2/0 3
## 7 2/1 1
## 8 2/2 29
## 9 3/3 1
## 10 <NA> 126812
##
## $SchPse2
## x freq
## 1 0/0 11064
## 2 0/1 241
## 3 0/2 5
## 4 0/3 1
## 5 1/0 245
## 6 1/1 1643
## 7 1/2 1
## 8 2/0 7
## 9 2/1 1
## 10 2/2 64
## 11 3/0 1
## 12 3/3 3
## 13 <NA> 124134
##
## $SchQua1
## x freq
## 1 0/0 20480
## 2 0/1 541
## 3 0/2 18
## 4 1/0 568
## 5 1/1 3390
## 6 1/2 2
## 7 2/0 9
## 8 2/1 7
## 9 2/2 92
## 10 3/3 1
## 11 <NA> 112302
##
## $SchQua2
## x freq
## 1 0/0 18244
## 2 0/1 721
## 3 0/2 14
## 4 1/0 754
## 5 1/1 3636
## 6 1/2 9
## 7 2/0 16
## 8 2/1 11
## 9 2/2 82
## 10 3/0 1
## 11 3/3 4
## 12 <NA> 113918
##
## $SchTri1
## x freq
## 1 0/0 8894
## 2 0/1 145
## 3 0/2 1
## 4 1/0 151
## 5 1/1 929
## 6 1/2 1
## 7 2/0 1
## 8 2/1 2
## 9 2/2 32
## 10 <NA> 127254
##
## $SchTri2
## x freq
## 1 0/0 7779
## 2 0/1 159
## 3 0/2 8
## 4 1/0 143
## 5 1/1 621
## 6 1/2 2
## 7 2/0 1
## 8 2/2 25
## 9 <NA> 128672
##
## $SchUnk
## x freq
## 1 0/0 23959
## 2 0/1 1288
## 3 0/2 28
## 4 0/3 1
## 5 1/0 1196
## 6 1/1 3695
## 7 1/2 11
## 8 2/0 29
## 9 2/1 8
## 10 2/2 91
## 11 3/0 1
## 12 3/3 3
## 13 <NA> 107100Counts by level of homozygosity and heterozygosity for each specimen
## $SchAre1
## x freq
## 1 0/0 8081
## 2 0/1 138
## 3 0/2 6
## 4 1/0 132
## 5 1/1 1607
## 6 1/2 3
## 7 2/0 1
## 8 2/1 2
## 9 2/2 51
## 10 3/0 1
## 11 3/3 1
## 12 <NA> 127387
##
## $SchAre2
## x freq
## 1 0/0 6482
## 2 0/1 121
## 3 0/2 2
## 4 1/0 103
## 5 1/1 1183
## 6 2/0 6
## 7 2/2 28
## 8 3/3 1
## 9 <NA> 129484
##
## $SchAur1
## x freq
## 1 0/0 10179
## 2 0/1 152
## 3 0/2 5
## 4 1/0 101
## 5 1/1 1480
## 6 2/0 7
## 7 2/1 2
## 8 2/2 39
## 9 3/3 3
## 10 <NA> 125442
##
## $SchAur2
## x freq
## 1 0/0 9552
## 2 0/1 186
## 3 0/2 2
## 4 1/0 142
## 5 1/1 1557
## 6 1/2 1
## 7 2/0 6
## 8 2/1 4
## 9 2/2 63
## 10 3/3 4
## 11 <NA> 125893
##
## $SchAuri1
## x freq
## 1 0/0 12807
## 2 0/1 357
## 3 0/2 14
## 4 1/0 336
## 5 1/1 1787
## 6 1/2 1
## 7 2/0 8
## 8 2/1 1
## 9 2/2 47
## 10 3/3 3
## 11 <NA> 122049
##
## $SchAuri2
## x freq
## 1 0/0 5396
## 2 0/1 67
## 3 1/0 50
## 4 1/1 835
## 5 1/2 1
## 6 2/0 2
## 7 2/2 21
## 8 3/3 2
## 9 <NA> 131036
##
## $SchAuri3
## x freq
## 1 0/0 5098
## 2 0/1 140
## 3 0/2 2
## 4 1/0 161
## 5 1/1 659
## 6 2/0 2
## 7 2/1 1
## 8 2/2 19
## 9 3/3 1
## 10 <NA> 131327
##
## $SchAuri4
## x freq
## 1 0/0 2975
## 2 0/1 44
## 3 1/0 21
## 4 1/1 245
## 5 2/0 1
## 6 2/2 4
## 7 <NA> 134120
##
## $SchAuri5
## x freq
## 1 0/0 4198
## 2 0/1 58
## 3 0/2 1
## 4 1/0 24
## 5 1/1 445
## 6 2/1 1
## 7 2/2 14
## 8 <NA> 132669
##
## $SchBol1
## x freq
## 1 0/0 10093
## 2 0/1 188
## 3 0/2 8
## 4 1/0 183
## 5 1/1 1265
## 6 2/0 3
## 7 2/2 37
## 8 3/3 1
## 9 <NA> 125632
##
## $SchBol2
## x freq
## 1 0/0 3458
## 2 0/1 49
## 3 1/0 43
## 4 1/1 323
## 5 2/0 1
## 6 2/2 6
## 7 3/3 1
## 8 <NA> 133529
##
## $SchBol4
## x freq
## 1 0/0 21273
## 2 0/1 1453
## 3 0/2 25
## 4 1/0 1415
## 5 1/1 3540
## 6 1/2 10
## 7 2/0 33
## 8 2/1 10
## 9 2/2 95
## 10 3/3 4
## 11 <NA> 109552
##
## $SchCom1
## x freq
## 1 0/0 14164
## 2 0/1 413
## 3 0/2 10
## 4 0/3 1
## 5 1/0 350
## 6 1/1 1784
## 7 1/2 5
## 8 2/0 10
## 9 2/1 3
## 10 2/2 44
## 11 3/3 3
## 12 <NA> 120623
##
## $SchCom2
## x freq
## 1 0/0 20393
## 2 0/1 695
## 3 0/2 18
## 4 1/0 697
## 5 1/1 2765
## 6 1/2 7
## 7 2/0 20
## 8 2/1 7
## 9 2/2 51
## 10 3/0 1
## 11 3/3 1
## 12 <NA> 112755
##
## $SchComp1
## x freq
## 1 0/0 12891
## 2 0/1 333
## 3 0/2 11
## 4 1/0 381
## 5 1/1 1990
## 6 1/2 4
## 7 1/3 1
## 8 2/0 12
## 9 2/1 3
## 10 2/2 35
## 11 3/3 2
## 12 <NA> 121747
##
## $SchComp2
## x freq
## 1 0/0 16431
## 2 0/1 808
## 3 0/2 18
## 4 0/3 1
## 5 1/0 826
## 6 1/1 2284
## 7 1/2 3
## 8 2/0 30
## 9 2/1 6
## 10 2/2 70
## 11 3/3 2
## 12 <NA> 116931
##
## $SchCompA1
## x freq
## 1 0/0 13981
## 2 0/1 309
## 3 0/2 6
## 4 1/0 313
## 5 1/1 2148
## 6 1/2 1
## 7 2/0 5
## 8 2/1 3
## 9 2/2 56
## 10 2/3 1
## 11 <NA> 120587
##
## $SchCompA2
## x freq
## 1 0/0 9347
## 2 0/1 197
## 3 0/2 3
## 4 1/0 180
## 5 1/1 1045
## 6 2/0 4
## 7 2/1 1
## 8 2/2 39
## 9 <NA> 126594
##
## $SchCra1
## x freq
## 1 0/0 10778
## 2 0/1 246
## 3 0/2 5
## 4 1/0 264
## 5 1/1 1726
## 6 1/2 2
## 7 2/0 11
## 8 2/1 3
## 9 2/2 60
## 10 3/0 1
## 11 3/3 3
## 12 <NA> 124311
##
## $SchCras1
## x freq
## 1 0/0 16464
## 2 0/1 256
## 3 0/2 9
## 4 1/0 242
## 5 1/1 2401
## 6 1/2 1
## 7 2/0 4
## 8 2/1 2
## 9 2/2 79
## 10 3/2 1
## 11 <NA> 117951
##
## $SchCras2
## x freq
## 1 0/0 21521
## 2 0/1 1088
## 3 0/2 23
## 4 0/3 1
## 5 1/0 1051
## 6 1/1 2745
## 7 1/2 2
## 8 2/0 25
## 9 2/1 5
## 10 2/2 68
## 11 <NA> 110881
##
## $SchCusAur1
## x freq
## 1 0/0 11628
## 2 0/1 227
## 3 0/2 9
## 4 1/0 208
## 5 1/1 1703
## 6 1/2 6
## 7 2/0 7
## 8 2/1 3
## 9 2/2 47
## 10 3/3 1
## 11 <NA> 123571
##
## $SchCusAur2
## x freq
## 1 0/0 19239
## 2 0/1 671
## 3 0/2 17
## 4 0/3 1
## 5 1/0 554
## 6 1/1 2334
## 7 1/2 3
## 8 2/0 20
## 9 2/1 3
## 10 2/2 68
## 11 3/3 1
## 12 <NA> 114499
##
## $SchCusB1
## x freq
## 1 0/0 12732
## 2 0/1 365
## 3 0/2 7
## 4 1/0 349
## 5 1/1 1799
## 6 1/2 3
## 7 2/0 8
## 8 2/1 5
## 9 2/2 55
## 10 3/0 2
## 11 3/3 2
## 12 <NA> 122083
##
## $SchCusB2
## x freq
## 1 0/0 21823
## 2 0/1 746
## 3 0/2 19
## 4 0/3 1
## 5 1/0 738
## 6 1/1 2758
## 7 1/2 2
## 8 2/0 25
## 9 2/1 4
## 10 2/2 67
## 11 3/3 5
## 12 <NA> 111222
##
## $SchCusDn1
## x freq
## 1 0/0 4502
## 2 0/1 88
## 3 1/0 75
## 4 1/1 463
## 5 2/2 13
## 6 <NA> 132269
##
## $SchCusDn2
## x freq
## 1 0/0 14974
## 2 0/1 536
## 3 0/2 18
## 4 1/0 596
## 5 1/1 2238
## 6 1/2 5
## 7 2/0 13
## 8 2/1 3
## 9 2/2 49
## 10 3/3 1
## 11 <NA> 118977
##
## $SchCusDn3
## x freq
## 1 0/0 32215
## 2 0/1 2017
## 3 0/2 37
## 4 0/3 2
## 5 1/0 2019
## 6 1/1 6132
## 7 1/2 18
## 8 2/0 60
## 9 2/1 14
## 10 2/2 183
## 11 3/0 2
## 12 3/1 2
## 13 3/3 6
## 14 <NA> 94703
##
## $SchCusDr1
## x freq
## 1 0/0 3816
## 2 0/1 49
## 3 1/0 30
## 4 1/1 604
## 5 2/0 1
## 6 2/2 13
## 7 <NA> 132897
##
## $SchCusDr2
## x freq
## 1 0/0 18915
## 2 0/1 1009
## 3 0/2 18
## 4 0/3 1
## 5 1/0 1037
## 6 1/1 3226
## 7 1/2 10
## 8 2/0 22
## 9 2/1 7
## 10 2/2 101
## 11 3/3 2
## 12 <NA> 113062
##
## $SchCusDr3
## x freq
## 1 0/0 7071
## 2 0/1 257
## 3 0/2 1
## 4 1/0 269
## 5 1/1 1528
## 6 1/2 2
## 7 2/0 6
## 8 2/1 1
## 9 2/2 37
## 10 3/3 1
## 11 <NA> 128237
##
## $SchCusEC1
## x freq
## 1 0/0 24910
## 2 0/1 1431
## 3 0/2 46
## 4 1/0 1412
## 5 1/1 4791
## 6 1/2 12
## 7 2/0 40
## 8 2/1 14
## 9 2/2 119
## 10 3/0 1
## 11 3/2 1
## 12 3/3 1
## 13 <NA> 104632
##
## $SchCusEC2
## x freq
## 1 0/0 15415
## 2 0/1 426
## 3 0/2 13
## 4 1/0 422
## 5 1/1 2311
## 6 1/2 3
## 7 2/0 17
## 8 2/1 4
## 9 2/2 50
## 10 3/1 1
## 11 3/3 3
## 12 <NA> 118745
##
## $SchCusEC3
## x freq
## 1 0/0 5266
## 2 0/1 84
## 3 0/2 2
## 4 1/0 75
## 5 1/1 878
## 6 1/2 1
## 7 2/0 2
## 8 2/2 35
## 9 <NA> 131067
##
## $SchCusEF1
## x freq
## 1 0/0 14270
## 2 0/1 340
## 3 0/2 14
## 4 1/0 320
## 5 1/1 1963
## 6 1/2 1
## 7 2/0 9
## 8 2/1 2
## 9 2/2 64
## 10 2/3 1
## 11 3/0 1
## 12 3/3 1
## 13 <NA> 120424
##
## $SchCusJ1
## x freq
## 1 0/0 12355
## 2 0/1 321
## 3 0/2 10
## 4 1/0 297
## 5 1/1 2065
## 6 1/2 3
## 7 2/0 13
## 8 2/1 4
## 9 2/2 69
## 10 3/3 3
## 11 <NA> 122270
##
## $SchCusJ2
## x freq
## 1 0/0 5790
## 2 0/1 53
## 3 0/2 2
## 4 1/0 58
## 5 1/1 712
## 6 2/2 19
## 7 <NA> 130776
##
## $SchCusJ3
## x freq
## 1 0/0 18004
## 2 0/1 434
## 3 0/2 12
## 4 1/0 432
## 5 1/1 2728
## 6 1/2 6
## 7 2/0 9
## 8 2/1 5
## 9 2/2 72
## 10 3/3 2
## 11 <NA> 115706
##
## $SchCusJ4
## x freq
## 1 0/0 10563
## 2 0/1 240
## 3 0/2 4
## 4 1/0 203
## 5 1/1 1197
## 6 1/2 1
## 7 2/0 6
## 8 2/1 2
## 9 2/2 25
## 10 3/3 2
## 11 <NA> 125167
##
## $SchCusJ5
## x freq
## 1 0/0 5117
## 2 0/1 129
## 3 0/2 1
## 4 1/0 120
## 5 1/1 659
## 6 2/2 18
## 7 3/0 1
## 8 3/3 1
## 9 <NA> 131364
##
## $SchCusLG2
## x freq
## 1 0/0 4473
## 2 0/1 71
## 3 0/2 2
## 4 1/0 48
## 5 1/1 408
## 6 1/2 2
## 7 2/0 1
## 8 2/2 18
## 9 <NA> 132387
##
## $SchCusP1
## x freq
## 1 0/0 13985
## 2 0/1 418
## 3 0/2 3
## 4 1/0 338
## 5 1/1 1553
## 6 2/0 16
## 7 2/1 7
## 8 2/2 53
## 9 3/3 2
## 10 <NA> 121035
##
## $SchCusP2
## x freq
## 1 0/0 8873
## 2 0/1 91
## 3 0/2 1
## 4 1/0 107
## 5 1/1 1178
## 6 1/2 2
## 7 2/0 4
## 8 2/2 26
## 9 3/3 1
## 10 <NA> 127127
##
## $SchEpi1
## x freq
## 1 0/0 13436
## 2 0/1 305
## 3 0/2 5
## 4 1/0 278
## 5 1/1 1522
## 6 1/2 1
## 7 2/0 5
## 8 2/1 4
## 9 2/2 50
## 10 3/3 2
## 11 <NA> 121802
##
## $SchEpi10
## x freq
## 1 0/0 10942
## 2 0/1 315
## 3 0/2 4
## 4 1/0 274
## 5 1/1 1591
## 6 1/2 3
## 7 2/0 6
## 8 2/1 3
## 9 2/2 50
## 10 3/1 1
## 11 <NA> 124221
##
## $SchEpi11
## x freq
## 1 0/0 7581
## 2 0/1 154
## 3 0/2 6
## 4 1/0 164
## 5 1/1 723
## 6 2/0 3
## 7 2/2 27
## 8 3/2 1
## 9 3/3 1
## 10 <NA> 128750
##
## $SchEpi2
## x freq
## 1 0/0 7747
## 2 0/1 111
## 3 0/2 3
## 4 1/0 114
## 5 1/1 1051
## 6 1/2 1
## 7 2/0 2
## 8 2/1 1
## 9 2/2 29
## 10 3/3 1
## 11 <NA> 128350
##
## $SchEpi3
## x freq
## 1 0/0 9060
## 2 0/1 152
## 3 0/2 3
## 4 1/0 135
## 5 1/1 1436
## 6 2/0 4
## 7 2/1 1
## 8 2/2 53
## 9 3/0 1
## 10 3/3 3
## 11 <NA> 126562
##
## $SchEpi4
## x freq
## 1 0/0 16143
## 2 0/1 1162
## 3 0/2 37
## 4 1/0 1049
## 5 1/1 4091
## 6 1/2 14
## 7 2/0 25
## 8 2/1 18
## 9 2/2 109
## 10 3/0 1
## 11 3/3 3
## 12 <NA> 114758
##
## $SchEpi5
## x freq
## 1 0/0 8801
## 2 0/1 165
## 3 0/2 4
## 4 1/0 132
## 5 1/1 1210
## 6 2/0 2
## 7 2/1 2
## 8 2/2 38
## 9 3/3 2
## 10 <NA> 127054
##
## $SchEpi6
## x freq
## 1 0/0 9945
## 2 0/1 247
## 3 0/2 6
## 4 1/0 245
## 5 1/1 1705
## 6 1/2 2
## 7 2/0 9
## 8 2/1 1
## 9 2/2 70
## 10 <NA> 125180
##
## $SchEpi7
## x freq
## 1 0/0 12889
## 2 0/1 195
## 3 0/2 2
## 4 1/0 162
## 5 1/1 2590
## 6 1/2 1
## 7 2/0 8
## 8 2/1 2
## 9 2/2 59
## 10 3/3 3
## 11 <NA> 121499
##
## $SchEpi8
## x freq
## 1 0/0 11178
## 2 0/1 236
## 3 0/2 2
## 4 1/0 222
## 5 1/1 1526
## 6 1/2 1
## 7 2/0 4
## 8 2/1 1
## 9 2/2 35
## 10 3/3 1
## 11 <NA> 124204
##
## $SchEpi9
## x freq
## 1 0/0 14964
## 2 0/1 622
## 3 0/2 18
## 4 1/0 620
## 5 1/1 2952
## 6 1/2 7
## 7 2/0 15
## 8 2/1 12
## 9 2/2 75
## 10 3/3 2
## 11 <NA> 118123
##
## $SchExi1
## x freq
## 1 0/0 3163
## 2 0/1 56
## 3 0/2 3
## 4 1/0 44
## 5 1/1 406
## 6 1/2 2
## 7 2/0 1
## 8 2/2 10
## 9 <NA> 133725
##
## $SchExi2
## x freq
## 1 0/0 15747
## 2 0/1 659
## 3 0/2 21
## 4 1/0 646
## 5 1/1 2099
## 6 1/2 3
## 7 2/0 21
## 8 2/1 4
## 9 2/2 55
## 10 3/3 2
## 11 <NA> 118153
##
## $SchExi3
## x freq
## 1 0/0 3419
## 2 0/1 57
## 3 1/0 49
## 4 1/1 283
## 5 2/0 1
## 6 2/1 1
## 7 2/2 15
## 8 <NA> 133585
##
## $SchExi4
## x freq
## 1 0/0 13740
## 2 0/1 342
## 3 0/2 10
## 4 0/3 1
## 5 1/0 349
## 6 1/1 1953
## 7 1/2 2
## 8 2/0 8
## 9 2/1 2
## 10 2/2 62
## 11 3/0 1
## 12 3/3 2
## 13 <NA> 120938
##
## $SchGra1
## x freq
## 1 0/0 11100
## 2 0/1 226
## 3 0/2 1
## 4 0/3 1
## 5 1/0 172
## 6 1/1 1483
## 7 1/2 1
## 8 2/0 4
## 9 2/1 1
## 10 2/2 37
## 11 3/3 3
## 12 <NA> 124381
##
## $SchGra2
## x freq
## 1 0/0 8079
## 2 0/1 217
## 3 0/2 2
## 4 1/0 185
## 5 1/1 1100
## 6 1/2 1
## 7 2/0 5
## 8 2/2 23
## 9 3/3 2
## 10 <NA> 127796
##
## $SchInc1
## x freq
## 1 0/0 9244
## 2 0/1 219
## 3 0/2 4
## 4 0/3 1
## 5 1/0 241
## 6 1/1 1568
## 7 1/2 3
## 8 1/3 2
## 9 2/0 7
## 10 2/1 2
## 11 2/2 69
## 12 3/0 1
## 13 3/3 2
## 14 <NA> 126047
##
## $SchLig1
## x freq
## 1 0/0 23308
## 2 0/1 1290
## 3 0/2 25
## 4 0/3 1
## 5 1/0 1259
## 6 1/1 3121
## 7 1/2 6
## 8 2/0 26
## 9 2/1 8
## 10 2/2 83
## 11 3/3 2
## 12 <NA> 108281
##
## $SchLim1
## x freq
## 1 0/0 22588
## 2 0/1 1721
## 3 0/2 42
## 4 0/3 1
## 5 1/0 1778
## 6 1/1 5267
## 7 1/2 19
## 8 2/0 57
## 9 2/1 29
## 10 2/2 155
## 11 3/0 2
## 12 3/1 1
## 13 3/3 4
## 14 <NA> 105746
##
## $SchLim2
## x freq
## 1 0/0 6878
## 2 0/1 133
## 3 0/2 4
## 4 1/0 130
## 5 1/1 1151
## 6 2/0 1
## 7 2/2 31
## 8 3/3 2
## 9 <NA> 129080
##
## $SchLim3
## x freq
## 1 0/0 3700
## 2 0/1 55
## 3 1/0 38
## 4 1/1 261
## 5 2/0 3
## 6 2/2 5
## 7 <NA> 133348
##
## $SchLor1
## x freq
## 1 0/0 10283
## 2 0/1 179
## 3 0/2 3
## 4 1/0 162
## 5 1/1 1158
## 6 2/0 2
## 7 2/1 1
## 8 2/2 35
## 9 3/3 1
## 10 <NA> 125586
##
## $SchLor2
## x freq
## 1 0/0 27009
## 2 0/1 2075
## 3 0/2 33
## 4 0/3 1
## 5 1/0 2150
## 6 1/1 5118
## 7 1/2 19
## 8 2/0 53
## 9 2/1 11
## 10 2/2 139
## 11 3/0 1
## 12 3/3 3
## 13 <NA> 100798
##
## $SchMeg1
## x freq
## 1 0/0 7157
## 2 0/1 121
## 3 0/2 5
## 4 1/0 128
## 5 1/1 1081
## 6 2/0 1
## 7 2/2 33
## 8 3/3 1
## 9 <NA> 128883
##
## $SchNig1
## x freq
## 1 0/0 9017
## 2 0/1 308
## 3 0/2 9
## 4 1/0 294
## 5 1/1 1653
## 6 1/2 4
## 7 2/0 12
## 8 2/1 4
## 9 2/2 65
## 10 3/3 2
## 11 <NA> 126042
##
## $SchPic1
## x freq
## 1 0/0 9421
## 2 0/1 275
## 3 0/2 12
## 4 1/0 246
## 5 1/1 1594
## 6 1/2 3
## 7 2/0 3
## 8 2/1 3
## 9 2/2 42
## 10 <NA> 125811
##
## $SchPic2
## x freq
## 1 0/0 6880
## 2 0/1 108
## 3 0/2 4
## 4 1/0 116
## 5 1/1 707
## 6 2/0 3
## 7 2/1 1
## 8 2/2 14
## 9 3/3 2
## 10 <NA> 129575
##
## $SchPic3
## x freq
## 1 0/0 10173
## 2 0/1 207
## 3 0/2 4
## 4 1/0 192
## 5 1/1 1324
## 6 1/3 1
## 7 2/0 4
## 8 2/1 2
## 9 2/2 38
## 10 3/3 1
## 11 <NA> 125464
##
## $SchPic4
## x freq
## 1 0/0 8158
## 2 0/1 167
## 3 0/2 5
## 4 1/0 127
## 5 1/1 1340
## 6 1/2 1
## 7 2/0 3
## 8 2/2 29
## 9 3/3 1
## 10 <NA> 127579
##
## $SchPse1
## x freq
## 1 0/0 9329
## 2 0/1 131
## 3 0/2 1
## 4 1/0 95
## 5 1/1 1008
## 6 2/0 3
## 7 2/1 1
## 8 2/2 29
## 9 3/3 1
## 10 <NA> 126812
##
## $SchPse2
## x freq
## 1 0/0 11064
## 2 0/1 241
## 3 0/2 5
## 4 0/3 1
## 5 1/0 245
## 6 1/1 1643
## 7 1/2 1
## 8 2/0 7
## 9 2/1 1
## 10 2/2 64
## 11 3/0 1
## 12 3/3 3
## 13 <NA> 124134
##
## $SchQua1
## x freq
## 1 0/0 20480
## 2 0/1 541
## 3 0/2 18
## 4 1/0 568
## 5 1/1 3390
## 6 1/2 2
## 7 2/0 9
## 8 2/1 7
## 9 2/2 92
## 10 3/3 1
## 11 <NA> 112302
##
## $SchQua2
## x freq
## 1 0/0 18244
## 2 0/1 721
## 3 0/2 14
## 4 1/0 754
## 5 1/1 3636
## 6 1/2 9
## 7 2/0 16
## 8 2/1 11
## 9 2/2 82
## 10 3/0 1
## 11 3/3 4
## 12 <NA> 113918
##
## $SchTri1
## x freq
## 1 0/0 8894
## 2 0/1 145
## 3 0/2 1
## 4 1/0 151
## 5 1/1 929
## 6 1/2 1
## 7 2/0 1
## 8 2/1 2
## 9 2/2 32
## 10 <NA> 127254
##
## $SchTri2
## x freq
## 1 0/0 7779
## 2 0/1 159
## 3 0/2 8
## 4 1/0 143
## 5 1/1 621
## 6 1/2 2
## 7 2/0 1
## 8 2/2 25
## 9 <NA> 128672
##
## $SchUnk
## x freq
## 1 0/0 23959
## 2 0/1 1288
## 3 0/2 28
## 4 0/3 1
## 5 1/0 1196
## 6 1/1 3695
## 7 1/2 11
## 8 2/0 29
## 9 2/1 8
## 10 2/2 91
## 11 3/0 1
## 12 3/3 3
## 13 <NA> 107100Compare homozygote to heterozygote frequences for 6 alleles per loci
#Total homozygotes for 6 alleles per loci
(homozygote.alleles.6<-sum(homozygote.0.0.count.sum, homozygote.1.1.count.sum, homozygote.2.2.count.sum, homozygote.3.3.count.sum))## [1] 1102229#Total heterozygotes for 6 alleles per loci
(heterozygote.alleles.6<-sum(heterozygote.0.1.count.sum, heterozygote.0.2.count.sum, heterozygote.0.3.count.sum, heterozygote.1.0.count.sum,
heterozygote.2.0.count.sum, heterozygote.3.0.count.sum, heterozygote.1.2.count.sum, heterozygote.1.3.count.sum, heterozygote.2.1.count.sum,
heterozygote.3.1.count.sum))## [1] 66333#Comparison of homozygotes to heterozygotes for alleles=6; 16 fold more homozygotes
(homo.heterozygote.6.com<-round(homozygote.alleles.6/heterozygote.alleles.6,2))## [1] 16.62Overall heterozygote genotype counts for alleles = 4 and allleles = 6 runs
## Alleles 6 Alleles 4 Difference between 6 and 4
## 0/1 32606 30108 2498
## 0/2 756 691 65
## 0/3 16 16 0
## 1/0 31575 29130 2445
## 2/0 834 773 61
## 3/0 20 19 1
## 1/2 241 233 8
## 1/3 4 4 0
## 2/1 276 259 17
## 3/1 5 4 1Percentage of 0/1 and 1/0 calls out of all heterozygote calls
## [1] 97Tammy’s comment
- Of the heterozygote alleles that would be dropped from going from an alleles=6 to an alleles=4 run, 97% (4943 SNPS) are either 1/0 or 0/1 genotypes.
Compare homozygote to heterozygote frequences for 4 alleles per loci
# compare homozygote to heterozygote frequences for 4 alleles per loci
#Total homozygotes for 4 alleles per loci
(homozygote.alleles.4<-sum(homozygote.alleles.4.0.0.count.sum, homozygote.alleles.4.1.1.count.sum, homozygote.alleles.4.2.2.count.sum, homozygote.alleles.4.3.3.count.sum))## [1] 1065495#Total heterozygotes for 6 alleles per loci
(heterozygote.alleles.4<-sum(heterozygote.alleles.4.0.1.count.sum, heterozygote.alleles.4.0.2.count.sum, heterozygote.alleles.4.0.3.count.sum, heterozygote.alleles.4.1.0.count.sum,
heterozygote.alleles.4.2.0.count.sum, heterozygote.alleles.4.3.0.count.sum, heterozygote.alleles.4.1.2.count.sum, heterozygote.alleles.4.1.3.count.sum, heterozygote.alleles.4.2.1.count.sum,
heterozygote.alleles.4.3.1.count.sum))## [1] 61237#Comparison of homozygotes to heterozygotes for alleles=4; 17 fold more homozygotes
(homo.heterozygote.alleles.4.com<-round(homozygote.alleles.4/heterozygote.alleles.4,2))## [1] 17.4#Difference between homozygosity and heterozygosity levels
homo.diff<-homozygote.alleles.6-homozygote.alleles.4
hetero.diff<-heterozygote.alleles.6-heterozygote.alleles.4Table whowing difference between homozygotes and heterozygotes for alleles=6 and alleles=4 runs
## Alleles = 4 Alleles = 6 Difference between 6 and 4
## Homozygous 1065495 1102229 36734
## Heterozygous 61237 66333 5096Tammy’s comment
By using the alleles = 4 instead of alleles =6 per loci filter, we loose 5096 heterozygous SNPs.
List with the differences in genotypes between the alleles=6 per loci and alleles=4 per loci ipyrad runs
## $SchAre1
## $SchAre1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchAre1$`Genotype freq: alleles=6`
## [1] 8035 137 6 132 1598 3 1 2 51 1
## [11] 1 123226
##
## $SchAre1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchAre1$`Genotype freq: alleles=4`
## [1] 8035 137 6 132 1598 3 1 2 51 1
## [11] 1 123226
##
## $SchAre1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchAre2
## $SchAre2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchAre2$`Genotype freq: alleles=6`
## [1] 6476 121 2 103 1174 6 27 1 125283
##
## $SchAre2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchAre2$`Genotype freq: alleles=4`
## [1] 6476 121 2 103 1174 6 27 1 125283
##
## $SchAre2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchAur1
## $SchAur1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchAur1$`Genotype freq: alleles=6`
## [1] 9909 145 5 100 1438 7 2 38 3 121546
##
## $SchAur1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchAur1$`Genotype freq: alleles=4`
## [1] 9909 145 5 100 1438 7 2 38 3 121546
##
## $SchAur1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchAur2
## $SchAur2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchAur2$`Genotype freq: alleles=6`
## [1] 9351 185 2 142 1514 1 6 4 60 4
## [11] 121924
##
## $SchAur2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchAur2$`Genotype freq: alleles=4`
## [1] 9351 185 2 142 1514 1 6 4 60 4
## [11] 121924
##
## $SchAur2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchAuri1
## $SchAuri1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchAuri1$`Genotype freq: alleles=6`
## [1] 12093 306 12 297 1729 1 7 1 46 3
## [11] 118698
##
## $SchAuri1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchAuri1$`Genotype freq: alleles=4`
## [1] 12093 306 12 297 1729 1 7 1 46 3
## [11] 118698
##
## $SchAuri1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchAuri2
## $SchAuri2$`Genotypes: alleles=6`
## [1] 0/0 0/1 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchAuri2$`Genotype freq: alleles=6`
## [1] 5318 67 49 827 1 2 21 2 126906
##
## $SchAuri2$`Genotypes: alleles=4`
## [1] 0/0 0/1 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchAuri2$`Genotype freq: alleles=4`
## [1] 5318 67 49 827 1 2 21 2 126906
##
## $SchAuri2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchAuri3
## $SchAuri3$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchAuri3$`Genotype freq: alleles=6`
## [1] 5080 138 1 156 651 2 1 19 1 127144
##
## $SchAuri3$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchAuri3$`Genotype freq: alleles=4`
## [1] 5080 138 1 156 651 2 1 19 1 127144
##
## $SchAuri3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchAuri4
## $SchAuri4$`Genotypes: alleles=6`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2
##
## $SchAuri4$`Genotype freq: alleles=6`
## [1] 2919 43 21 239 1 3 129967
##
## $SchAuri4$`Genotypes: alleles=4`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2
##
## $SchAuri4$`Genotype freq: alleles=4`
## [1] 2919 43 21 239 1 3 129967
##
## $SchAuri4$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0
##
##
## $SchAuri5
## $SchAuri5$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/1 2/2
##
## $SchAuri5$`Genotype freq: alleles=6`
## [1] 4174 58 1 24 437 1 14 128484
##
## $SchAuri5$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/1 2/2
##
## $SchAuri5$`Genotype freq: alleles=4`
## [1] 4174 58 1 24 437 1 14 128484
##
## $SchAuri5$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0
##
##
## $SchBol1
## $SchBol1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchBol1$`Genotype freq: alleles=6`
## [1] 9193 163 7 148 1226 1 36 1 122418
##
## $SchBol1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchBol1$`Genotype freq: alleles=4`
## [1] 9193 163 7 148 1226 1 36 1 122418
##
## $SchBol1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchBol2
## $SchBol2$`Genotypes: alleles=6`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2 3/3
##
## $SchBol2$`Genotype freq: alleles=6`
## [1] 3353 47 43 316 1 6 1 129426
##
## $SchBol2$`Genotypes: alleles=4`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2 3/3
##
## $SchBol2$`Genotype freq: alleles=4`
## [1] 3353 47 43 316 1 6 1 129426
##
## $SchBol2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0
##
##
## $SchBol4
## $SchBol4$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchBol4$`Genotype freq: alleles=6`
## [1] 20230 1284 23 1274 3453 10 29 10 94 4
## [11] 106782
##
## $SchBol4$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchBol4$`Genotype freq: alleles=4`
## [1] 20230 1284 23 1274 3453 10 29 10 94 4
## [11] 106782
##
## $SchBol4$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCom1
## $SchCom1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCom1$`Genotype freq: alleles=6`
## [1] 13011 359 10 1 288 1674 5 9 3 41
## [11] 3 117789
##
## $SchCom1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCom1$`Genotype freq: alleles=4`
## [1] 13011 359 10 1 288 1674 5 9 3 41
## [11] 3 117789
##
## $SchCom1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCom2
## $SchCom2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchCom2$`Genotype freq: alleles=6`
## [1] 18999 622 14 636 2676 7 19 5 49 1
## [11] 1 110164
##
## $SchCom2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchCom2$`Genotype freq: alleles=4`
## [1] 18999 622 14 636 2676 7 19 5 49 1
## [11] 1 110164
##
## $SchCom2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchComp1
## $SchComp1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/3
##
## $SchComp1$`Genotype freq: alleles=6`
## [1] 12604 325 11 374 1940 4 1 12 3 34
## [11] 2 117883
##
## $SchComp1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/3
##
## $SchComp1$`Genotype freq: alleles=4`
## [1] 12604 325 11 374 1940 4 1 12 3 34
## [11] 2 117883
##
## $SchComp1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchComp2
## $SchComp2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchComp2$`Genotype freq: alleles=6`
## [1] 15240 635 14 1 649 2252 3 22 6 69
## [11] 2 114300
##
## $SchComp2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchComp2$`Genotype freq: alleles=4`
## [1] 15240 635 14 1 649 2252 3 22 6 69
## [11] 2 114300
##
## $SchComp2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCompA1
## $SchCompA1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3
##
## $SchCompA1$`Genotype freq: alleles=6`
## [1] 13512 290 5 293 2089 1 4 2 55 1
## [11] 116941
##
## $SchCompA1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3
##
## $SchCompA1$`Genotype freq: alleles=4`
## [1] 13512 290 5 293 2089 1 4 2 55 1
## [11] 116941
##
## $SchCompA1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCompA2
## $SchCompA2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2
##
## $SchCompA2$`Genotype freq: alleles=6`
## [1] 8608 164 3 152 1001 3 1 34 123227
##
## $SchCompA2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2
##
## $SchCompA2$`Genotype freq: alleles=4`
## [1] 8608 164 3 152 1001 3 1 34 123227
##
## $SchCompA2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchCra1
## $SchCra1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchCra1$`Genotype freq: alleles=6`
## [1] 10687 242 5 260 1710 2 11 3 59 1
## [11] 3 120210
##
## $SchCra1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchCra1$`Genotype freq: alleles=4`
## [1] 10687 242 5 260 1710 2 11 3 59 1
## [11] 3 120210
##
## $SchCra1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCras1
## $SchCras1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/2
##
## $SchCras1$`Genotype freq: alleles=6`
## [1] 15819 240 9 234 2343 1 4 2 78 1
## [11] 114462
##
## $SchCras1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/2
##
## $SchCras1$`Genotype freq: alleles=4`
## [1] 15819 240 9 234 2343 1 4 2 78 1
## [11] 114462
##
## $SchCras1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCras2
## $SchCras2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchCras2$`Genotype freq: alleles=6`
## [1] 19966 847 17 1 810 2685 1 20 5 66
## [11] 108775
##
## $SchCras2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchCras2$`Genotype freq: alleles=4`
## [1] 19966 847 17 1 810 2685 1 20 5 66
## [11] 108775
##
## $SchCras2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusAur1
## $SchCusAur1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusAur1$`Genotype freq: alleles=6`
## [1] 10830 213 9 191 1615 5 7 3 47 1
## [11] 120272
##
## $SchCusAur1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusAur1$`Genotype freq: alleles=4`
## [1] 10830 213 9 191 1615 5 7 3 47 1
## [11] 120272
##
## $SchCusAur1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusAur2
## $SchCusAur2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusAur2$`Genotype freq: alleles=6`
## [1] 17993 614 17 1 505 2234 2 20 3 65
## [11] 1 111738
##
## $SchCusAur2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusAur2$`Genotype freq: alleles=4`
## [1] 17993 614 17 1 505 2234 2 20 3 65
## [11] 1 111738
##
## $SchCusAur2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusB1
## $SchCusB1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchCusB1$`Genotype freq: alleles=6`
## [1] 12313 364 6 346 1777 3 8 5 54 2
## [11] 2 118313
##
## $SchCusB1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchCusB1$`Genotype freq: alleles=4`
## [1] 12313 364 6 346 1777 3 8 5 54 2
## [11] 2 118313
##
## $SchCusB1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusB2
## $SchCusB2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusB2$`Genotype freq: alleles=6`
## [1] 20056 644 15 1 635 2665 2 21 3 64
## [11] 5 109082
##
## $SchCusB2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusB2$`Genotype freq: alleles=4`
## [1] 20056 644 15 1 635 2665 2 21 3 64
## [11] 5 109082
##
## $SchCusB2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusDn1
## $SchCusDn1$`Genotypes: alleles=6`
## [1] 0/0 0/1 1/0 1/1 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/2
##
## $SchCusDn1$`Genotype freq: alleles=6`
## [1] 4502 88 75 463 13 128052
##
## $SchCusDn1$`Genotypes: alleles=4`
## [1] 0/0 0/1 1/0 1/1 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/2
##
## $SchCusDn1$`Genotype freq: alleles=4`
## [1] 4502 88 75 463 13 128052
##
## $SchCusDn1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0
##
##
## $SchCusDn2
## $SchCusDn2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusDn2$`Genotype freq: alleles=6`
## [1] 14519 502 16 557 2181 5 13 3 47 1
## [11] 115349
##
## $SchCusDn2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusDn2$`Genotype freq: alleles=4`
## [1] 14519 502 16 557 2181 5 13 3 47 1
## [11] 115349
##
## $SchCusDn2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusDn3
## $SchCusDn3$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3
##
## $SchCusDn3$`Genotype freq: alleles=6`
## [1] 31302 1946 34 2 1960 6008 16 58 14 175 2
## [12] 1 6 91669
##
## $SchCusDn3$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3
##
## $SchCusDn3$`Genotype freq: alleles=4`
## [1] 31302 1946 34 2 1960 6008 16 58 14 175 2
## [12] 1 6 91669
##
## $SchCusDn3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusDr1
## $SchCusDr1$`Genotypes: alleles=6`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2
##
## $SchCusDr1$`Genotype freq: alleles=6`
## [1] 3770 49 30 598 1 13 128732
##
## $SchCusDr1$`Genotypes: alleles=4`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2
##
## $SchCusDr1$`Genotype freq: alleles=4`
## [1] 3770 49 30 598 1 13 128732
##
## $SchCusDr1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0
##
##
## $SchCusDr2
## $SchCusDr2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusDr2$`Genotype freq: alleles=6`
## [1] 18325 875 17 1 900 3171 10 19 7 98
## [11] 2 109768
##
## $SchCusDr2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusDr2$`Genotype freq: alleles=4`
## [1] 18325 875 17 1 900 3171 10 19 7 98
## [11] 2 109768
##
## $SchCusDr2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusDr3
## $SchCusDr3$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusDr3$`Genotype freq: alleles=6`
## [1] 6783 244 1 251 1470 2 6 1 34 1
## [11] 124400
##
## $SchCusDr3$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusDr3$`Genotype freq: alleles=4`
## [1] 6783 244 1 251 1470 2 6 1 34 1
## [11] 124400
##
## $SchCusDr3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusEC1
## $SchCusEC1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/2 3/3
##
## $SchCusEC1$`Genotype freq: alleles=6`
## [1] 24204 1306 43 1289 4715 11 33 14 116 1
## [11] 1 1 101459
##
## $SchCusEC1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/2 3/3
##
## $SchCusEC1$`Genotype freq: alleles=4`
## [1] 24204 1306 43 1289 4715 11 33 14 116 1
## [11] 1 1 101459
##
## $SchCusEC1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusEC2
## $SchCusEC2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1 3/3
##
## $SchCusEC2$`Genotype freq: alleles=6`
## [1] 15280 414 13 411 2299 3 17 4 50 1
## [11] 3 114698
##
## $SchCusEC2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1 3/3
##
## $SchCusEC2$`Genotype freq: alleles=4`
## [1] 15280 414 13 411 2299 3 17 4 50 1
## [11] 3 114698
##
## $SchCusEC2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusEC3
## $SchCusEC3$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchCusEC3$`Genotype freq: alleles=6`
## [1] 5054 81 2 68 863 1 2 35 127087
##
## $SchCusEC3$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchCusEC3$`Genotype freq: alleles=4`
## [1] 5054 81 2 68 863 1 2 35 127087
##
## $SchCusEC3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchCusEF1
## $SchCusEF1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3 3/0 3/3
##
## $SchCusEF1$`Genotype freq: alleles=6`
## [1] 13598 310 12 286 1900 1 9 2 61 1
## [11] 1 1 117011
##
## $SchCusEF1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 2/3 3/0 3/3
##
## $SchCusEF1$`Genotype freq: alleles=4`
## [1] 13598 310 12 286 1900 1 9 2 61 1
## [11] 1 1 117011
##
## $SchCusEF1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusJ1
## $SchCusJ1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusJ1$`Genotype freq: alleles=6`
## [1] 12180 310 10 285 2041 3 13 4 67 3
## [11] 118277
##
## $SchCusJ1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusJ1$`Genotype freq: alleles=4`
## [1] 12180 310 10 285 2041 3 13 4 67 3
## [11] 118277
##
## $SchCusJ1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusJ2
## $SchCusJ2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/2
##
## $SchCusJ2$`Genotype freq: alleles=6`
## [1] 5560 53 2 58 682 16 126822
##
## $SchCusJ2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/2
##
## $SchCusJ2$`Genotype freq: alleles=4`
## [1] 5560 53 2 58 682 16 126822
##
## $SchCusJ2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0
##
##
## $SchCusJ3
## $SchCusJ3$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusJ3$`Genotype freq: alleles=6`
## [1] 17442 429 12 424 2649 6 9 4 70 2
## [11] 112146
##
## $SchCusJ3$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusJ3$`Genotype freq: alleles=4`
## [1] 17442 429 12 424 2649 6 9 4 70 2
## [11] 112146
##
## $SchCusJ3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusJ4
## $SchCusJ4$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusJ4$`Genotype freq: alleles=6`
## [1] 10297 239 4 202 1184 1 6 2 25 2
## [11] 121231
##
## $SchCusJ4$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchCusJ4$`Genotype freq: alleles=4`
## [1] 10297 239 4 202 1184 1 6 2 25 2
## [11] 121231
##
## $SchCusJ4$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusJ5
## $SchCusJ5$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/2 3/0 3/3
##
## $SchCusJ5$`Genotype freq: alleles=6`
## [1] 5028 125 1 120 642 17 1 1 127258
##
## $SchCusJ5$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/2 3/0 3/3
##
## $SchCusJ5$`Genotype freq: alleles=4`
## [1] 5028 125 1 120 642 17 1 1 127258
##
## $SchCusJ5$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchCusLG2
## $SchCusLG2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchCusLG2$`Genotype freq: alleles=6`
## [1] 4270 71 2 48 390 2 1 17 128392
##
## $SchCusLG2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchCusLG2$`Genotype freq: alleles=4`
## [1] 4270 71 2 48 390 2 1 17 128392
##
## $SchCusLG2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchCusP1
## $SchCusP1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchCusP1$`Genotype freq: alleles=6`
## [1] 12929 354 2 263 1501 13 5 49 2 118075
##
## $SchCusP1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchCusP1$`Genotype freq: alleles=4`
## [1] 12929 354 2 263 1501 13 5 49 2 118075
##
## $SchCusP1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchCusP2
## $SchCusP2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchCusP2$`Genotype freq: alleles=6`
## [1] 8645 91 1 99 1156 2 4 25 1 123169
##
## $SchCusP2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchCusP2$`Genotype freq: alleles=4`
## [1] 8645 91 1 99 1156 2 4 25 1 123169
##
## $SchCusP2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi1
## $SchEpi1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi1$`Genotype freq: alleles=6`
## [1] 12860 273 5 252 1473 1 5 4 50 2
## [11] 118268
##
## $SchEpi1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi1$`Genotype freq: alleles=4`
## [1] 12860 273 5 252 1473 1 5 4 50 2
## [11] 118268
##
## $SchEpi1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi10
## $SchEpi10$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1
##
## $SchEpi10$`Genotype freq: alleles=6`
## [1] 10913 311 4 268 1582 3 5 3 50 1
## [11] 120053
##
## $SchEpi10$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/1
##
## $SchEpi10$`Genotype freq: alleles=4`
## [1] 10913 311 4 268 1582 3 5 3 50 1
## [11] 120053
##
## $SchEpi10$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi11
## $SchEpi11$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/2 3/3
##
## $SchEpi11$`Genotype freq: alleles=6`
## [1] 7520 146 5 155 718 3 27 1 1 124617
##
## $SchEpi11$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/2 3/3
##
## $SchEpi11$`Genotype freq: alleles=4`
## [1] 7520 146 5 155 718 3 27 1 1 124617
##
## $SchEpi11$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi2
## $SchEpi2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi2$`Genotype freq: alleles=6`
## [1] 7688 111 3 113 1047 1 2 1 29 1
## [11] 124197
##
## $SchEpi2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi2$`Genotype freq: alleles=4`
## [1] 7688 111 3 113 1047 1 2 1 29 1
## [11] 124197
##
## $SchEpi2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi3
## $SchEpi3$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/0 3/3
##
## $SchEpi3$`Genotype freq: alleles=6`
## [1] 8897 148 3 130 1409 4 1 50 1 3
## [11] 122547
##
## $SchEpi3$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/0 3/3
##
## $SchEpi3$`Genotype freq: alleles=4`
## [1] 8897 148 3 130 1409 4 1 50 1 3
## [11] 122547
##
## $SchEpi3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi4
## $SchEpi4$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchEpi4$`Genotype freq: alleles=6`
## [1] 15670 1079 32 977 4019 13 24 17 107 1
## [11] 3 111251
##
## $SchEpi4$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchEpi4$`Genotype freq: alleles=4`
## [1] 15670 1079 32 977 4019 13 24 17 107 1
## [11] 3 111251
##
## $SchEpi4$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi5
## $SchEpi5$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchEpi5$`Genotype freq: alleles=6`
## [1] 8744 163 4 129 1198 2 2 38 2 122911
##
## $SchEpi5$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchEpi5$`Genotype freq: alleles=4`
## [1] 8744 163 4 129 1198 2 2 38 2 122911
##
## $SchEpi5$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi6
## $SchEpi6$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchEpi6$`Genotype freq: alleles=6`
## [1] 9815 239 5 230 1672 2 9 1 70 121150
##
## $SchEpi6$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchEpi6$`Genotype freq: alleles=4`
## [1] 9815 239 5 230 1672 2 9 1 70 121150
##
## $SchEpi6$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi7
## $SchEpi7$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi7$`Genotype freq: alleles=6`
## [1] 12387 191 2 160 2545 1 8 2 57 3
## [11] 117837
##
## $SchEpi7$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi7$`Genotype freq: alleles=4`
## [1] 12387 191 2 160 2545 1 8 2 57 3
## [11] 117837
##
## $SchEpi7$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi8
## $SchEpi8$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi8$`Genotype freq: alleles=6`
## [1] 10918 235 2 221 1505 1 4 1 35 1
## [11] 120270
##
## $SchEpi8$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi8$`Genotype freq: alleles=4`
## [1] 10918 235 2 221 1505 1 4 1 35 1
## [11] 120270
##
## $SchEpi8$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchEpi9
## $SchEpi9$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi9$`Genotype freq: alleles=6`
## [1] 14806 607 18 601 2922 7 15 11 73 2
## [11] 114131
##
## $SchEpi9$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchEpi9$`Genotype freq: alleles=4`
## [1] 14806 607 18 601 2922 7 15 11 73 2
## [11] 114131
##
## $SchEpi9$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchExi1
## $SchExi1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchExi1$`Genotype freq: alleles=6`
## [1] 3154 56 3 44 406 2 1 10 129517
##
## $SchExi1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchExi1$`Genotype freq: alleles=4`
## [1] 3154 56 3 44 406 2 1 10 129517
##
## $SchExi1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchExi2
## $SchExi2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchExi2$`Genotype freq: alleles=6`
## [1] 14042 534 18 529 2001 3 18 4 52 2
## [11] 115990
##
## $SchExi2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchExi2$`Genotype freq: alleles=4`
## [1] 14042 534 18 529 2001 3 18 4 52 2
## [11] 115990
##
## $SchExi2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchExi3
## $SchExi3$`Genotypes: alleles=6`
## [1] 0/0 0/1 1/0 1/1 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/1 2/2
##
## $SchExi3$`Genotype freq: alleles=6`
## [1] 3379 55 47 277 1 1 15 129418
##
## $SchExi3$`Genotypes: alleles=4`
## [1] 0/0 0/1 1/0 1/1 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/1 2/2
##
## $SchExi3$`Genotype freq: alleles=4`
## [1] 3379 55 47 277 1 1 15 129418
##
## $SchExi3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0
##
##
## $SchExi4
## $SchExi4$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchExi4$`Genotype freq: alleles=6`
## [1] 13662 341 10 1 344 1936 2 8 2 62
## [11] 1 2 116822
##
## $SchExi4$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchExi4$`Genotype freq: alleles=4`
## [1] 13662 341 10 1 344 1936 2 8 2 62
## [11] 1 2 116822
##
## $SchExi4$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchGra1
## $SchGra1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchGra1$`Genotype freq: alleles=6`
## [1] 11021 225 1 1 171 1477 1 4 1 37
## [11] 3 120251
##
## $SchGra1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchGra1$`Genotype freq: alleles=4`
## [1] 11021 225 1 1 171 1477 1 4 1 37
## [11] 3 120251
##
## $SchGra1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchGra2
## $SchGra2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchGra2$`Genotype freq: alleles=6`
## [1] 8010 216 2 184 1096 1 5 23 2 123654
##
## $SchGra2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchGra2$`Genotype freq: alleles=4`
## [1] 8010 216 2 184 1096 1 5 23 2 123654
##
## $SchGra2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchInc1
## $SchInc1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/0 3/3
##
## $SchInc1$`Genotype freq: alleles=6`
## [1] 9135 213 4 1 235 1553 2 2 7 2
## [11] 68 1 2 121968
##
## $SchInc1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 1/3 2/0 2/1 2/2 3/0 3/3
##
## $SchInc1$`Genotype freq: alleles=4`
## [1] 9135 213 4 1 235 1553 2 2 7 2
## [11] 68 1 2 121968
##
## $SchInc1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchLig1
## $SchLig1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchLig1$`Genotype freq: alleles=6`
## [1] 21598 1160 24 1 1137 3001 6 25 7 83
## [11] 1 106150
##
## $SchLig1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchLig1$`Genotype freq: alleles=4`
## [1] 21598 1160 24 1 1137 3001 6 25 7 83
## [11] 1 106150
##
## $SchLig1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchLim1
## $SchLim1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3
##
## $SchLim1$`Genotype freq: alleles=6`
## [1] 21847 1586 37 1 1651 5205 19 55 26 152
## [11] 2 1 4 102607
##
## $SchLim1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/1 3/3
##
## $SchLim1$`Genotype freq: alleles=4`
## [1] 21847 1586 37 1 1651 5205 19 55 26 152
## [11] 2 1 4 102607
##
## $SchLim1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchLim2
## $SchLim2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchLim2$`Genotype freq: alleles=6`
## [1] 6659 127 4 126 1132 1 30 2 125112
##
## $SchLim2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchLim2$`Genotype freq: alleles=4`
## [1] 6659 127 4 126 1132 1 30 2 125112
##
## $SchLim2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchLim3
## $SchLim3$`Genotypes: alleles=6`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2
##
## $SchLim3$`Genotype freq: alleles=6`
## [1] 3675 54 38 261 3 5 129157
##
## $SchLim3$`Genotypes: alleles=4`
## [1] 0/0 0/1 1/0 1/1 2/0 2/2 <NA>
## Levels: 0/0 0/1 1/0 1/1 2/0 2/2
##
## $SchLim3$`Genotype freq: alleles=4`
## [1] 3675 54 38 261 3 5 129157
##
## $SchLim3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0
##
##
## $SchLor1
## $SchLor1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchLor1$`Genotype freq: alleles=6`
## [1] 10118 178 3 162 1140 2 1 35 1 121553
##
## $SchLor1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchLor1$`Genotype freq: alleles=4`
## [1] 10118 178 3 162 1140 2 1 35 1 121553
##
## $SchLor1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchLor2
## $SchLor2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchLor2$`Genotype freq: alleles=6`
## [1] 25963 1945 29 1 2009 5043 19 48 9 138 3
## [12] 97986
##
## $SchLor2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchLor2$`Genotype freq: alleles=4`
## [1] 25963 1945 29 1 2009 5043 19 48 9 138 3
## [12] 97986
##
## $SchLor2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchMeg1
## $SchMeg1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchMeg1$`Genotype freq: alleles=6`
## [1] 7139 121 5 128 1080 1 33 1 124685
##
## $SchMeg1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/2 3/3
##
## $SchMeg1$`Genotype freq: alleles=4`
## [1] 7139 121 5 128 1080 1 33 1 124685
##
## $SchMeg1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchNig1
## $SchNig1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchNig1$`Genotype freq: alleles=6`
## [1] 8935 300 9 283 1651 4 12 4 65 2
## [11] 121928
##
## $SchNig1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchNig1$`Genotype freq: alleles=4`
## [1] 8935 300 9 283 1651 4 12 4 65 2
## [11] 121928
##
## $SchNig1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchPic1
## $SchPic1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchPic1$`Genotype freq: alleles=6`
## [1] 9243 273 12 242 1580 3 3 3 42 121792
##
## $SchPic1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchPic1$`Genotype freq: alleles=4`
## [1] 9243 273 12 242 1580 3 3 3 42 121792
##
## $SchPic1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchPic2
## $SchPic2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchPic2$`Genotype freq: alleles=6`
## [1] 6843 101 4 114 705 3 1 14 2 125406
##
## $SchPic2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchPic2$`Genotype freq: alleles=4`
## [1] 6843 101 4 114 705 3 1 14 2 125406
##
## $SchPic2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchPic3
## $SchPic3$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/3 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/3 2/0 2/1 2/2 3/3
##
## $SchPic3$`Genotype freq: alleles=6`
## [1] 10038 203 4 182 1300 1 4 2 38 1
## [11] 121420
##
## $SchPic3$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/3 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/3 2/0 2/1 2/2 3/3
##
## $SchPic3$`Genotype freq: alleles=4`
## [1] 10038 203 4 182 1300 1 4 2 38 1
## [11] 121420
##
## $SchPic3$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchPic4
## $SchPic4$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchPic4$`Genotype freq: alleles=6`
## [1] 8120 156 5 121 1328 1 3 29 1 123429
##
## $SchPic4$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 3/3
##
## $SchPic4$`Genotype freq: alleles=4`
## [1] 8120 156 5 121 1328 1 3 29 1 123429
##
## $SchPic4$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchPse1
## $SchPse1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchPse1$`Genotype freq: alleles=6`
## [1] 9257 130 1 93 1001 3 1 29 1 122677
##
## $SchPse1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 2/0 2/1 2/2 3/3
##
## $SchPse1$`Genotype freq: alleles=4`
## [1] 9257 130 1 93 1001 3 1 29 1 122677
##
## $SchPse1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchPse2
## $SchPse2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchPse2$`Genotype freq: alleles=6`
## [1] 10997 238 5 1 244 1627 1 7 1 64
## [11] 1 3 120004
##
## $SchPse2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchPse2$`Genotype freq: alleles=4`
## [1] 10997 238 5 1 244 1627 1 7 1 64
## [11] 1 3 120004
##
## $SchPse2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchQua1
## $SchQua1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchQua1$`Genotype freq: alleles=6`
## [1] 20071 514 16 538 3356 2 9 6 91 1
## [11] 108589
##
## $SchQua1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/3
##
## $SchQua1$`Genotype freq: alleles=4`
## [1] 20071 514 16 538 3356 2 9 6 91 1
## [11] 108589
##
## $SchQua1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchQua2
## $SchQua2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchQua2$`Genotype freq: alleles=6`
## [1] 17858 681 11 712 3565 9 13 11 80 1
## [11] 4 110248
##
## $SchQua2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchQua2$`Genotype freq: alleles=4`
## [1] 17858 681 11 712 3565 9 13 11 80 1
## [11] 4 110248
##
## $SchQua2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0
##
##
## $SchTri1
## $SchTri1$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchTri1$`Genotype freq: alleles=6`
## [1] 8427 135 1 143 895 1 1 2 32 123556
##
## $SchTri1$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/1 2/2
##
## $SchTri1$`Genotype freq: alleles=4`
## [1] 8427 135 1 143 895 1 1 2 32 123556
##
## $SchTri1$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0
##
##
## $SchTri2
## $SchTri2$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchTri2$`Genotype freq: alleles=6`
## [1] 7757 157 8 139 618 2 1 25 124486
##
## $SchTri2$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2 <NA>
## Levels: 0/0 0/1 0/2 1/0 1/1 1/2 2/0 2/2
##
## $SchTri2$`Genotype freq: alleles=4`
## [1] 7757 157 8 139 618 2 1 25 124486
##
## $SchTri2$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0
##
##
## $SchUnk
## $SchUnk$`Genotypes: alleles=6`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchUnk$`Genotype freq: alleles=6`
## [1] 22679 1166 26 1 1090 3583 11 27 7 88
## [11] 1 3 104511
##
## $SchUnk$`Genotypes: alleles=4`
## [1] 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3 <NA>
## Levels: 0/0 0/1 0/2 0/3 1/0 1/1 1/2 2/0 2/1 2/2 3/0 3/3
##
## $SchUnk$`Genotype freq: alleles=4`
## [1] 22679 1166 26 1 1090 3583 11 27 7 88
## [11] 1 3 104511
##
## $SchUnk$`Frequency difference alleles 6-4`
## [1] 0 0 0 0 0 0 0 0 0 0 0 0 0Comparison of allele filtering runs
This table compares the different ipyrad runs based on filtering of alleles.
- left column has been filtered for six alleles
- second column has been filtered for four alleles
- third column has been filtered for two alleles
- fourth column is a percentage comparing the two allele to six allele totals. Higher values indicate a higher percentage of loci with two alleles at a site that passed through filtering.
- fifth column is a percentage comparing the two allele to four allele totals. Higher values indicate a higher percentage of loci with two alleles at a site that passed through filtering.
## Sample alleles=6 alleles=4 alleles=2 % 2/6 % 2/4
## 1 SchAre1 10043 9987 7998 79.64 80.08
## 2 SchAre2 7931 7915 6714 84.66 84.83
## 3 SchAur1 11990 11666 9356 78.03 80.20
## 4 SchAur2 11552 11302 9226 79.86 81.63
## 5 SchAuri1 15384 14516 8824 57.36 60.79
## 6 SchAuri2 6393 6304 5322 83.25 84.42
## 7 SchAuri3 6098 6064 4626 75.86 76.29
## 8 SchAuri4 3292 3228 2539 77.13 78.66
## 9 SchAuri5 4745 4713 3573 75.30 75.81
## 10 SchBol1 11797 10789 7023 59.53 65.09
## 11 SchBol2 3890 3776 2835 72.88 75.08
## 12 SchBol4 27888 26440 16895 60.58 63.90
## 13 SchCom1 16832 15449 9493 56.40 61.45
## 14 SchCom2 24685 23058 14171 57.41 61.46
## 15 SchComp1 15690 15337 12165 77.53 79.32
## 16 SchComp2 20510 18923 13197 64.34 69.74
## 17 SchCompA1 16847 16275 11393 67.63 70.00
## 18 SchCompA2 10841 9988 7599 70.10 76.08
## 19 SchCra1 13125 13008 9919 75.57 76.25
## 20 SchCras1 19477 18745 13713 70.41 73.16
## 21 SchCras2 26558 24446 14977 56.39 61.27
## 22 SchCusAur1 13842 12924 7823 56.52 60.53
## 23 SchCusAur2 22946 21486 13689 59.66 63.71
## 24 SchCusB1 15349 14902 11323 73.77 75.98
## 25 SchCusB2 26235 24152 15665 59.71 64.86
## 26 SchCusDn1 5148 5148 3883 75.43 75.43
## 27 SchCusDn2 18445 17856 11696 63.41 65.50
## 28 SchCusDn3 42757 41572 29001 67.83 69.76
## 29 SchCusDr1 4518 4466 3380 74.81 75.68
## 30 SchCusDr2 24396 23467 15801 64.77 67.33
## 31 SchCusDr3 9176 8796 5162 56.26 58.69
## 32 SchCusEC1 32858 31808 21171 64.43 66.56
## 33 SchCusEC2 18701 18531 14384 76.92 77.62
## 34 SchCusEC3 6357 6120 4742 74.59 77.48
## 35 SchCusEF1 17020 16215 10505 61.72 64.79
## 36 SchCusJ1 15178 14953 11062 72.88 73.98
## 37 SchCusJ2 6637 6374 4422 66.63 69.38
## 38 SchCusJ3 21735 21075 14660 67.45 69.56
## 39 SchCusJ4 12285 12004 8635 70.29 71.93
## 40 SchCusJ5 6053 5942 4490 74.18 75.56
## 41 SchCusLG2 5033 4811 3738 74.27 77.70
## 42 SchCusP1 16401 15143 10507 64.06 69.39
## 43 SchCusP2 10295 10036 6598 64.09 65.74
## 44 SchEpi1 15623 14939 9941 63.63 66.54
## 45 SchEpi10 13205 13156 10328 78.21 78.50
## 46 SchEpi11 8671 8585 7338 84.63 85.47
## 47 SchEpi2 9082 9018 7239 79.71 80.27
## 48 SchEpi3 10863 10660 8209 75.57 77.01
## 49 SchEpi4 22677 21966 14907 65.74 67.86
## 50 SchEpi5 10377 10301 8309 80.07 80.66
## 51 SchEpi6 12247 12057 9745 79.57 80.82
## 52 SchEpi7 15936 15379 12394 77.77 80.59
## 53 SchEpi8 13229 12943 10194 77.06 78.76
## 54 SchEpi9 19315 19090 14538 75.27 76.16
## 55 SchExi1 3696 3687 2758 74.62 74.80
## 56 SchExi2 19283 17224 10161 52.69 58.99
## 57 SchExi3 3829 3779 2909 75.97 76.98
## 58 SchExi4 16512 16408 13041 78.98 79.48
## 59 SchGra1 13052 12965 10352 79.31 79.85
## 60 SchGra2 9628 9553 7689 79.86 80.49
## 61 SchInc1 11386 11247 9077 79.72 80.71
## 62 SchLig1 29151 27065 16214 55.62 59.91
## 63 SchLim1 31721 30641 20225 63.76 66.01
## 64 SchLim2 8335 8086 5815 69.77 71.91
## 65 SchLim3 4065 4039 3152 77.54 78.04
## 66 SchLor1 11851 11664 9007 76.00 77.22
## 67 SchLor2 36665 35252 23132 63.09 65.62
## 68 SchMeg1 8539 8520 6978 81.72 81.90
## 69 SchNig1 11376 11273 8683 76.33 77.02
## 70 SchPic1 11621 11423 8960 77.10 78.44
## 71 SchPic2 7850 7802 6432 81.94 82.44
## 72 SchPic3 11974 11799 9700 81.01 82.21
## 73 SchPic4 9853 9786 7787 79.03 79.57
## 74 SchPse1 10611 10529 8475 79.87 80.49
## 75 SchPse2 13295 13203 10941 82.29 82.87
## 76 SchQua1 25141 24637 16825 66.92 68.29
## 77 SchQua2 23518 22971 15765 67.03 68.63
## 78 SchTri1 10166 9647 7795 76.68 80.80
## 79 SchTri2 8767 8736 7548 86.10 86.40
## 80 SchUnk 30361 28731 17527 57.73 61.00Distribution of alternative alleles in dataset
- left hand figure has at least four samples per loci
- center figure has at least ten samples per loci
- right hand side figure has at least twenty samples per loci
Heatmaps showing sampling coverage
- Samples as columns and loci as rows
Four samples per loci
Ten samples per loci
Twenty samples per loci
