Title: Loci coverage: full dataset
Name: Tammy L. Elliott
Date: June 19, 2019
R version 3.5.1
Loci coverage per specimen across various minimum depths of loci
This is the minimum number of samples that must have data at a given locus for it to be retained in the final data set. I set the maximum number of unique alleles allowed in (individual) consens reads after accounting for sequencing errors as two for these preliminary analyses.
Low-coverage samples to be excluded from further analyses
Below are listed samples that do not meet specific thresholds for the minimum number of loci to be included in further analyses.
Four samples per loci - less than 1500 loci recovered
These are the samples that did not have 1500 loci recovered when the minimum number of samples per loci was set at four. Sample names are listed in the first column.
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20
## 37 auritus-245 1240 689 636 616
## 38 auritus-306 957 729 679 651
## 39 auritus-307 724 599 574 552
## 42 australis-265 1098 746 669 645
## 47 bolusii-324 784 609 542 519
## 82 cuspidatus-260 1289 742 620 593
## 100 exilis-189 872 699 650 621
## 102 exilis-293 855 676 638 619
## 110 galpinii-235 1117 600 499 482
## 112 galpinii-239 1168 599 478 446
## 128 limosus-247 780 615 576 560
## mindepth_30
## 37 586
## 38 621
## 39 528
## 42 619
## 47 490
## 82 563
## 100 589
## 102 592
## 110 453
## 112 425
## 128 538Ten samples per loci - less than 700 loci recovered
These are the samples that did not have 700 loci recovered when the minimum number of samples per loci was set at ten. Sample names are listed in the first column.
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20
## 28 apogon-AK282169 1613 606 196 81
## 37 auritus-245 1240 689 636 616
## 39 auritus-307 724 599 574 552
## 47 bolusii-324 784 609 542 519
## 54 caespitans-AK288575 1741 440 192 95
## 100 exilis-189 872 699 650 621
## 102 exilis-293 855 676 638 619
## 110 galpinii-235 1117 600 499 482
## 112 galpinii-239 1168 599 478 446
## 128 limosus-247 780 615 576 560
## 141 nitens-AK308188 1800 572 238 113
## 143 pauciflorus-AK308186 2047 551 262 128
## 144 pauciflorus-AK308190 2249 698 256 114
## mindepth_30
## 28 51
## 37 586
## 39 528
## 47 490
## 54 66
## 100 589
## 102 592
## 110 453
## 112 425
## 128 538
## 141 82
## 143 91
## 144 79Fifteen samples per loci - less than 600 loci recovered
These are the samples that did not have 600 loci recovered when the minimum number of samples per loci was set at fifteen. Sample names are listed in the first column.
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20
## 28 apogon-AK282169 1613 606 196 81
## 29 apogon-AK308178 2400 728 298 152
## 39 auritus-307 724 599 574 552
## 47 bolusii-324 784 609 542 519
## 54 caespitans-AK288575 1741 440 192 95
## 68 concinuus-AK308197 1946 708 305 143
## 109 fluitans-AK289622 5120 1140 376 173
## 110 galpinii-235 1117 600 499 482
## 112 galpinii-239 1168 599 478 446
## 128 limosus-247 780 615 576 560
## 135 maschalinus-AK283575 3259 770 298 145
## 136 maschalinus-AK308198 3690 838 354 174
## 141 nitens-AK308188 1800 572 238 113
## 142 pauciflorus-AK284668 4086 947 267 122
## 143 pauciflorus-AK308186 2047 551 262 128
## 144 pauciflorus-AK308190 2249 698 256 114
## mindepth_30
## 28 51
## 29 115
## 39 528
## 47 490
## 54 66
## 68 102
## 109 108
## 110 453
## 112 425
## 128 538
## 135 106
## 136 122
## 141 82
## 142 67
## 143 91
## 144 79Twenty samples per loci - less than 600 loci recovered
These are the samples that did not have 600 loci recovered when the minimum number of samples per loci was set at twenty. Sample names are listed in the first column.
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20
## 28 apogon-AK282169 1613 606 196 81
## 29 apogon-AK308178 2400 728 298 152
## 39 auritus-307 724 599 574 552
## 47 bolusii-324 784 609 542 519
## 54 caespitans-AK288575 1741 440 192 95
## 68 concinuus-AK308197 1946 708 305 143
## 82 cuspidatus-260 1289 742 620 593
## 109 fluitans-AK289622 5120 1140 376 173
## 110 galpinii-235 1117 600 499 482
## 112 galpinii-239 1168 599 478 446
## 128 limosus-247 780 615 576 560
## 135 maschalinus-AK283575 3259 770 298 145
## 136 maschalinus-AK308198 3690 838 354 174
## 141 nitens-AK308188 1800 572 238 113
## 142 pauciflorus-AK284668 4086 947 267 122
## 143 pauciflorus-AK308186 2047 551 262 128
## 144 pauciflorus-AK308190 2249 698 256 114
## mindepth_30
## 28 51
## 29 115
## 39 528
## 47 490
## 54 66
## 68 102
## 82 563
## 109 108
## 110 453
## 112 425
## 128 538
## 135 106
## 136 122
## 141 82
## 142 67
## 143 91
## 144 79Thirty samples per loci - less than 600 loci recovered
These are the samples that did not have 600 loci recovered when the minimum number of samples per loci was set at thirty. Sample names are listed in the first column.
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20
## 28 apogon-AK282169 1613 606 196 81
## 29 apogon-AK308178 2400 728 298 152
## 37 auritus-245 1240 689 636 616
## 39 auritus-307 724 599 574 552
## 47 bolusii-324 784 609 542 519
## 54 caespitans-AK288575 1741 440 192 95
## 68 concinuus-AK308197 1946 708 305 143
## 82 cuspidatus-260 1289 742 620 593
## 100 exilis-189 872 699 650 621
## 102 exilis-293 855 676 638 619
## 109 fluitans-AK289622 5120 1140 376 173
## 110 galpinii-235 1117 600 499 482
## 112 galpinii-239 1168 599 478 446
## 128 limosus-247 780 615 576 560
## 135 maschalinus-AK283575 3259 770 298 145
## 136 maschalinus-AK308198 3690 838 354 174
## 141 nitens-AK308188 1800 572 238 113
## 142 pauciflorus-AK284668 4086 947 267 122
## 143 pauciflorus-AK308186 2047 551 262 128
## 144 pauciflorus-AK308190 2249 698 256 114
## mindepth_30
## 28 51
## 29 115
## 37 586
## 39 528
## 47 490
## 54 66
## 68 102
## 82 563
## 100 589
## 102 592
## 109 108
## 110 453
## 112 425
## 128 538
## 135 106
## 136 122
## 141 82
## 142 67
## 143 91
## 144 79Overlap of samples across different thresholds of minimum number of samples per loci
Low-coverage samples in minimum depth of four loci analysis, but not in minimum depth if 10
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20
## 1 auritus-306 957 729 679 651
## 2 australis-265 1098 746 669 645
## 3 cuspidatus-260 1289 742 620 593
## mindepth_30
## 1 621
## 2 619
## 3 563Low-coverage samples in minimum depth of ten loci analysis, but not in minimum depth if 15
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20 mindepth_30
## 1 auritus-245 1240 689 636 616 586
## 2 exilis-189 872 699 650 621 589
## 3 exilis-293 855 676 638 619 592Low-coverage samples in minimum depth of four loci analysis, but not in minimum depth if 15
## X mindepth_4 mindepth_10 mindepth_15 mindepth_20
## 1 auritus-245 1240 689 636 616
## 2 auritus-306 957 729 679 651
## 3 australis-265 1098 746 669 645
## 4 cuspidatus-260 1289 742 620 593
## 5 exilis-189 872 699 650 621
## 6 exilis-293 855 676 638 619
## mindepth_30
## 1 586
## 2 621
## 3 619
## 4 563
## 5 589
## 6 592Removal of samples because of low number recovered per loci
I have removed samples that have met any of the criteria below (22 samples removed in total):
- default parametres; miniumum depth per loci 4 samples
- default parametres; miniumum depth per loci 10 samples
- default parametres; miniumum depth per loci 15 samples
- default parametres; miniumum depth per loci 20 samples
- default parametres; miniumum depth per loci 30 samples
## [1] auritus-245 auritus-306 auritus-307
## [4] australis-265 bolusii-324 cuspidatus-260
## [7] exilis-189 exilis-293 galpinii-235
## [10] galpinii-239 limosus-247 apogon-AK282169
## [13] caespitans-AK288575 nitens-AK308188 pauciflorus-AK308186
## [16] pauciflorus-AK308190 apogon-AK308178 concinuus-AK308197
## [19] fluitans-AK289622 maschalinus-AK283575 maschalinus-AK308198
## [22] pauciflorus-AK284668
## 178 Levels: adnatus-DEB5531 albovaginatus-381 ... triticoides-281Additional samples removed from analyses and rationale
Probable contamination:
- Cya_hexandra-MM6368 (comes out with S. crassus)
- Cap_brevicaulis-209 (contamination with neovillosus-207)
- cuspidatus-423 contamination with compar-425
- bolusii-329
Number mix-ups:
- arenicola-MM6477; number mix-up
- crassus-MM6468; number mix-up
- Tet_capillacea-MM6467; number mix-up
Other:
- crassiculmis-420 - empty well
- Tet_unknown-MM6446 - unsure of identification (including genera) because of lack of access to voucher