Built data using BWA to estimate CentC (Centromereic tandem satellite repeat of 156 bp) abundance in sequenced maize lines from Jiao et al (2012)
Get raw data from tab delimited table.
setwd("/Users/Sid/Projects/CRM_mapping/CRM_files")
x = read.table("Jiao_CentC_abundance_sid.txt", header = T)
print(x)
## Filename Line ReadsTotal ReadsAligned
## 1 SRR448305 CAU06_zong31 70220186 260520
## 2 SRR448306 CAU07_D340 66386695 195593
## 3 SRR448307 CAU08_H127 62268851 80551
## 4 SRR448310 CAU10_yu87-1 73665999 343879
## 5 SRR448311 CAU100_shen5005 12737323 49179
## 6 SRR448312 CAU103_807D 16300981 41193
## 7 SRR448313 CAU105_1145 24718544 66898
## 8 SRR448314 CAU105_1145 30565005 86723
## 9 SRR448315 CAU107_D15 53675656 198572
## 10 SRR448316 CAU11_longkang11 71102163 303269
## 11 SRR448317 CAU112_S22 27845753 89273
## 12 SRR448318 CAU114_Q1261 43456299 227633
## 13 SRR448319 CAU115_ye52106 50490277 141159
## 14 SRR448320 CAU116_1205A 54764200 170816
## 15 SRR448321 CAU118_K12 66030692 252396
## 16 SRR448322 CAU12_danhuang02 70336140 283288
## 17 SRR448324 CAU120_xing230 37385244 109922
## 18 SRR448325 CAU125_K22 27629220 103414
## 19 SRR448326 CAU125_K22 30776709 118201
## 20 SRR448328 CAU129_P007 24566122 77848
## 21 SRR448332 CAU131_Yd6 39416761 149157
## 22 SRR448333 CAU132_IA5125 34932498 104530
## 23 SRR448334 CAU133_liao2202 11502078 31370
## 24 SRR448336 CAU134_dai6 31280492 102582
## 25 SRR448337 CAU137_W499 34393708 171602
## 26 SRR448338 CAU14_shen137 47486913 106263
## 27 SRR448340 CAU140_XOP2 44223532 184246
## 28 SRR448341 CAU142_D20 38019353 121439
## 29 SRR448342 CAU143_hai1134 42870887 177015
## 30 SRR448343 CAU144_yu374 32233566 109602
## 31 SRR448344 CAU146_dan9064 49369181 192125
## 32 SRR448345 CAU147_niu2-1 13538012 47922
## 33 SRR448346 CAU148_suwan1611 43960228 163656
## 34 SRR448347 CAU149_R017 34030044 130890
## 35 SRR448348 CAU15_zheng22 29773703 64439
## 36 SRR448349 CAU151_shen977 19930255 78011
## 37 SRR448350 CAU156_huangchangb 11487354 50438
## 38 SRR448351 CAU16_lv28 57673105 138587
## 39 SRR448352 CAU164_K10 19345929 47333
## 40 SRR448353 CAU165_ye5237 24707450 74702
## 41 SRR448354 CAU166_zheng32 52535130 148202
## 42 SRR448355 CAU17_huangC 57497000 182706
## 43 SRR448356 CAU173_P167 28674130 135954
## 44 SRR448357 CAU174_R31 23611655 113447
## 45 SRR448358 CAU178_changK 94898902 434250
## 46 SRR448359 CAU18_P138 20583574 30762
## 47 SRR448360 CAU180_M131-5 61677994 165462
## 48 SRR448361 CAU19_zi330 20203713 23887
## 49 SRR448362 CAU191_hai014 29485008 97956
## 50 SRR448363 CAU192_ji444 32386915 101957
## 51 SRR448364 CAU193_ben7884 26833842 94932
## 52 SRR448365 CAU194_huangyesi3 54763986 176722
## 53 SRR448366 CAU195_zaC546 26946562 46836
## 54 SRR448367 CAU197_4F1 54015843 326347
## 55 SRR448368 CAU198_wenhuang31413 40507939 183209
## 56 SRR448369 CAU199_ye515 28399048 151724
## 57 SRR448370 CAU20_huangzaosi 191108428 471562
## 58 SRR448371 CAU200_hu803 30856825 111139
## 59 SRR448372 CAU201_tian77 25134401 80587
## 60 SRR448373 CAU202_ye488 34013113 113031
## 61 SRR448388 CAU203_chang72 34950611 113877
## 62 SRR448389 CAU207_3H2 30424015 94969
## 63 SRR448390 CAU208_cheng698-3 45204675 80377
## 64 SRR448391 CAU21_tie7922 34600846 73624
## 65 SRR448392 CAU210_su75 22677405 63865
## 66 SRR448393 CAU211_Beck 24570811 64815
## 67 SRR448394 CAU215_P136 21826556 84290
## 68 SRR448395 CAU217_dan9046 110652778 277922
## 69 SRR448397 CAU224_W64a 28249653 83065
## 70 SRR448398 CAU225_A554 22544618 59010
## 71 SRR448399 CAU229_xun92-8 25270525 99061
## 72 SRR448400 CAU234_H21 887251 2473
## 73 SRR448401 CAU234_H21 16068895 40873
## 74 SRR448444 CAU235_shuang741 559589 2245
## 75 SRR448445 CAU235_shuang741 15585599 45571
## 76 SRR448446 CAU236_200B 1092877 3775
## 77 SRR448447 CAU236_200B 30213946 158700
## 78 SRR448490 CAU237_chong72 770165 1219
## 79 SRR448491 CAU237_chong72 15904038 35780
## 80 SRR448492 CAU238_Pa91 1329137 3815
## 81 SRR448493 CAU238_Pa91 17088412 57358
## 82 SRR448494 CAU239_yu537A 1133347 2273
## 83 SRR448495 CAU239_yu537A 17187114 58036
## 84 SRR448496 CAU24_9058 31221276 65416
## 85 SRR448497 CAU242_dan3115 38457502 195070
## 86 SRR448522 CAU244_zhonghuang64 37820345 130491
## 87 SRR448565 CAU247_dong327 19962688 68990
## 88 SRR448566 CAU248_698-3 40650765 101727
## 89 SRR448567 CAU248_698-3 23408604 59158
## 90 SRR448568 CAU25_ji853 32829141 154575
## 91 SRR448569 CAU251_N138 28308607 92283
## 92 SRR448570 CAU251_N138 27426825 88881
## 93 SRR448571 CAU254_DM07 15858528 36390
## 94 SRR448572 CAU254_DM07 28583023 64735
## 95 SRR448573 CAU256_B100 14947591 40343
## 96 SRR448576 CAU257_B98 60212549 268623
## 97 SRR448577 CAU261_lian87 18753302 56758
## 98 SRR448579 CAU264_L-1 23719370 49534
## 99 SRR448584 CAU271_changD 40051432 187246
## 100 SRR448592 CAU273_M101 29879889 75817
## 101 SRR448595 CAU275_B394 24173114 68002
## 102 SRR448597 CAU282_R25 20020800 55664
## 103 SRR448599 CAU282_R25 20382827 55533
## 104 SRR448600 CAU283_chengzi108 45166164 101062
## 105 SRR448601 CAU289_ye107 12277688 24802
## 106 SRR448603 CAU289_ye107 37128027 78747
## 107 SRR448604 CAU29_Maxa 23784872 71868
## 108 SRR448605 CAU290_jiutai1 35612329 107623
## 109 SRR448624 CAU294_hai9-21 24425785 65259
## 110 SRR448625 CAU295_ji533 16621982 36380
## 111 SRR448626 CAU297_ye832 11569584 14388
## 112 SRR448627 CAU302_B76 7816305 15783
## 113 SRR448628 CAU302_B76 15189089 67329
## 114 SRR448629 CAU303_NC268 10264447 12985
## 115 SRR448630 CAU303_NC268 19439394 24530
## 116 SRR448631 CAU306_Sg1533 6545604 7936
## 117 SRR448632 CAU306_Sg1533 13833698 37682
## 118 SRR448635 CAU310_7327 26323994 59452
## 119 SRR448636 CAU316_bao3040 28374877 131595
## 120 SRR448637 CAU320_Lx9801 1351975 2297
## 121 SRR448638 CAU320_Lx9801 14739661 82423
## 122 SRR448639 CAU326_shen135 72490424 197866
## 123 SRR448640 CAU332_baihe43 18218361 54439
## 124 SRR448641 CAU34_nan21-3 33345300 113218
## 125 SRR448642 CAU345_jiu138-5 49171391 200959
## 126 SRR448643 CAU347_ning55 29692827 80099
## 127 SRR448644 CAU350_han21 28291355 74765
## 128 SRR448645 CAU355_huotanghuang 33904579 122525
## 129 SRR448646 CAU357_yu82 24306236 64534
## 130 SRR448647 CAU359_CN165 20754591 57517
## 131 SRR448648 CAU361_fu8701 20774876 49348
## 132 SRR448649 CAU362_De811 15496102 38050
## 133 SRR448651 CAU365_shan89 22904421 61139
## 134 SRR448652 CAU366_A679 20135767 27335
## 135 SRR448653 CAU367_Va26 18801218 49254
## 136 SRR448654 CAU370_E28 15454342 35684
## 137 SRR448655 CAU372_zhongyin15 10654615 29423
## 138 SRR448656 CAU372_zhongyin15 16365886 48236
## 139 SRR448657 CAU375_zong3 22163836 122318
## 140 SRR448658 CAU382_FC-13 22841026 68706
## 141 SRR448659 CAU384_ji63 1262781 2461
## 142 SRR448660 CAU384_ji63 19468084 59586
## 143 SRR448661 CAU385_ji434 34082307 142149
## 144 SRR448662 CAU386_ji4112 1284580 1622
## 145 SRR448663 CAU386_ji4112 25486236 65808
## 146 SRR448664 CAU389_qi205 14425716 31486
## 147 SRR448665 CAU40_B68 13638572 48226
## 148 SRR448666 CAU400_P25 32415314 117880
## 149 SRR448667 CAU401_R98 26702796 80880
## 150 SRR448668 CAU402_qi319 9176761 20169
## 151 SRR448669 CAU402_qi319 17924690 36564
## 152 SRR448670 CAU405_huo17 28841800 94224
## 153 SRR448671 CAU409_huangyesi 37093956 120942
## 154 SRR448672 CAU411_shen142 21734757 47355
## 155 SRR448673 CAU413_siyi 19036920 34934
## 156 SRR448674 CAU416_xun971 15462457 60265
## 157 SRR448676 CAU420_Mo24W 33120955 95843
## 158 SRR448678 CAU422_W182bn 26009306 99748
## 159 SRR448679 CAU423_W153R 9777078 30990
## 160 SRR448680 CAU423_W153R 16824757 52227
## 161 SRR448682 CAU425_HP301 11084658 21554
## 162 SRR448684 CAU425_HP301 13859406 23750
## 163 SRR448685 CAU426_H84 17189062 52326
## 164 SRR448693 CAU429_tangsipingtou 38787828 90138
## 165 SRR448742 CAU434_cheng18 49272940 169222
## 166 SRR448743 CAU436_xinlun5-9 13084959 30095
## 167 SRR448744 CAU439_lv45 19311211 82233
## 168 SRR448745 CAU446_fengke1 16977653 53243
## 169 SRR448788 CAU448_ernan24 51042513 139373
## 170 SRR448789 CAU451_78371A 38269166 75738
## 171 SRR448790 CAU452_PHT10 27149205 110831
## 172 SRR448831 CAU453_PHH93 16415573 36245
## 173 SRR448832 CAU454_IBB14 17226995 35829
## 174 SRR448879 CAU458_LH149 3309522 2568
## 175 SRR448880 CAU458_LH149 25018117 45467
## 176 SRR448881 CAU461_794 7734986 10368
## 177 SRR448922 CAU461_794 30834640 42322
## 178 SRR448923 CAU463_PHR32 24228015 44805
## 179 SRR448924 CAU465_PHG50 2383596 5458
## 180 SRR448925 CAU465_PHG50 27007207 111611
## 181 SRR448926 CAU466_LH51 24417690 48626
## 182 SRR448927 CAU468_78010 24898674 85154
## 183 SRR448928 CAU470_LH39 47103161 97225
## 184 SRR448929 CAU471_PHG84 19108803 43219
## 185 SRR448930 CAU475_LH57 1320756 2806
## 186 SRR448931 CAU475_LH57 32340579 130549
## 187 SRR448935 CAU476_LH38 7391516 17476
## 188 SRR448937 CAU476_LH38 25278387 97169
## 189 SRR448938 CAU488_807 3143064 4620
## 190 SRR448939 CAU488_807 44471476 281850
## 191 SRR448940 CAU489_OH43 34759023 80829
## 192 SRR448941 CAU490_PHN11 27765047 68999
## 193 SRR448942 CAU491_PHJ70 15360449 36073
## 194 SRR448943 CAU492_DJ7 14545485 18975
## 195 SRR448944 CAU496_790 15964608 26492
## 196 SRR448945 CAU497_PHZ51 11057461 25083
## 197 SRR448946 CAU497_PHZ51 37099552 150044
## 198 SRR448947 CAU498_PHT60 14620594 29412
## 199 SRR448948 CAU501_PHG83 24887576 65110
## 200 SRR448950 CAU503_PHJ75 24187584 38488
## 201 SRR448951 CAU505_PB80 21949464 28734
## 202 SRR448952 CAU510_LH52 2438422 3198
## 203 SRR448953 CAU510_LH52 25145770 155354
## 204 SRR448954 CAU513_PHW52 10101211 24381
## 205 SRR448955 CAU513_PHW52 19176245 47285
## 206 SRR448956 CAU514_LH93 17886202 34698
## 207 SRR448957 CAU515_PHM57 18103181 43457
## 208 SRR448958 CAU517_LH60 11517747 22631
## 209 SRR448959 CAU518_PHG71 6427348 7240
## 210 SRR448960 CAU518_PHG71 20754061 25059
## 211 SRR448961 CAU520_Q381 5625580 8406
## 212 SRR448962 CAU520_Q381 34875669 101555
## 213 SRR448963 CAU521_MBPM 3765418 5318
## 214 SRR449014 CAU521_MBPM 38730008 206704
## 215 SRR449015 CAU522_PHW03 4237780 5922
## 216 SRR449016 CAU522_PHW03 42496750 262430
## 217 SRR449084 CAU523_PHW43 4698036 5502
## 218 SRR449085 CAU523_PHW43 24875573 125121
## 219 SRR449086 CAU525_LH190 19367353 32003
## 220 SRR449087 CAU526_B47 16624648 36488
## 221 SRR449088 CAU527_PHV78 33792310 105332
## 222 SRR449089 CAU528 26704943 42697
## 223 SRR449090 CAU530_PHK76 15586167 28763
## 224 SRR449091 CAU531_LH1 28823487 63353
## 225 SRR449093 CAU534_PHJ31 6808305 16719
## 226 SRR449094 CAU534_PHJ31 26943072 240800
## 227 SRR449095 CAU535_78002A 12329211 18015
## 228 SRR449096 CAU536_792 15532611 17591
## 229 SRR449097 CAU537_PHJ40 14269066 26334
## 230 SRR449098 CAU538_LH54 29737076 50808
## 231 SRR449099 CAU539_FAPW 13815918 25404
## 232 SRR449100 CAU541_LH205 6665347 8295
## 233 SRR449101 CAU541_LH205 26842651 154029
## 234 SRR449102 CAU542_LH127 6477159 10485
## 235 SRR449103 CAU542_LH127 31737530 243310
## 236 SRR449104 CAU545_LH194 8904610 7332
## 237 SRR449105 CAU545_LH194 23459266 104948
## 238 SRR449106 CAU546_LH202 12749890 13538
## 239 SRR449107 CAU549_RS710 5357410 6908
## 240 SRR449108 CAU549_RS710 37020729 173611
## 241 SRR449109 CAU551_PHW51 4181714 5434
## 242 SRR449111 CAU551_PHW51 33734762 283466
## 243 SRR449112 CAU566_PHP85 2186580 2866
## 244 SRR449113 CAU566_PHP85 40715994 172228
## 245 SRR449114 CAU572_LH143 45251745 111625
## 246 SRR449115 CAU574_207 32057836 88246
## 247 SRR449116 CAU575_CR1HT 22266283 54949
## 248 SRR449117 CAU576_6103 31176593 77119
## 249 SRR449118 CAU578_4676A 22171802 48314
## 250 SRR449119 CAU580_PHR36 15165187 35569
## 251 SRR449120 CAU582_IB02 20362418 86736
## 252 SRR449121 CAU583_IBB15 60631994 227658
## 253 SRR449122 CAU584_787 23909393 81391
## 254 SRR449123 CAU586_11430 31886535 106007
## 255 SRR449124 CAU587_2369 21544298 49676
## 256 SRR449125 CAU588_2MA22 17974364 62014
## 257 SRR449126 CAU590_MBST 41341981 120985
## 258 SRR449127 CAU591_PHN47 27884488 63528
## 259 SRR449128 CAU592_NS501 19970813 37723
## 260 SRR449129 CAU593_H8431 19612514 52832
## 261 SRR449130 CAU594_S8324 22411308 36022
## 262 SRR449131 CAU595_CR14 20019742 38858
## 263 SRR449132 CAU596_WIL901 18022392 43180
## 264 SRR449179 CAU597_WIL903 20377465 55931
## 265 SRR449180 CAU598_WIL500 15765492 23848
## 266 SRR449181 CAU599_E8501 27138560 59024
## 267 SRR449183 CAU601_L135 16290430 31524
## 268 SRR449184 CAU604_PHM10 7783949 8887
## 269 SRR449185 CAU604_PHM10 36025004 124748
## 270 SRR449186 CAU605_PHN82 10175370 16346
## 271 SRR449187 CAU605_PHN82 43682226 167014
## 272 SRR449188 CAU607_PHR63 9367487 23415
## 273 SRR449189 CAU607_PHR63 45047375 176995
## 274 SRR449190 CAU610_PHW20 3260782 4202
## 275 SRR449191 CAU610_PHW20 38413005 159107
## 276 SRR449192 CAU611_W23 15964139 17655
## 277 SRR449193 CAU631_PHP55 9445162 17526
## 278 SRR449194 CAU631_PHP55 38110651 159715
## 279 SRR449195 CAU638_huobai 36451636 75508
## 280 SRR449196 CAU69_qi410 1353005 4707
## 281 SRR449198 CAU77_DH149 28236717 71201
## 282 SRR449199 CAU78_R08 30134306 81824
## 283 SRR449200 CAU84_B95 32188304 87104
## 284 SRR449201 CAU84_B95 50933727 164287
## 285 SRR449202 CAU97_guan17-1 13353754 47108
## 286 SRR449203 CAU98_wu125 9470095 28921
## 287 SRR449204 CAU98_wu125 24648419 61833
## 288 SRR449205 CAU31_wu126 3671863 11343
## 289 SRR449206 CAU31_wu126 30743618 173046
## 290 SRR449207 CAU33_yi36 19094166 63282
## 291 SRR449208 CAU39_CM105 35389492 115096
## 292 SRR449209 CAU41_P39 21084501 86747
## 293 SRR449210 CAU42_shangyin110-1 31504085 107373
## 294 SRR449211 CAU46_zhong451 23256779 88283
## 295 SRR449212 CAU47_huotanghuang17 8949639 34509
## 296 SRR449213 CAU47_huotanghuang17 38994479 195179
## 297 SRR449214 CAU58_B12 55059522 241682
## 298 SRR449215 CAU609_PHV37 39491933 195459
## 299 SRR449216 CAU61_ji870 12808349 47745
## 300 SRR449217 CAU63_fu8521 2012682 6362
## 301 SRR449218 CAU63_fu8521 21413888 37534
## 302 SRR449219 CAU68_jiao05 39059217 143145
## 303 SRR449244 CAU73_xiangai3 67539877 237137
## 304 SRR449245 CAU74_fusheA 49431847 279349
## 305 SRR449246 CAU76_qiong51 56229192 162022
## 306 SRR449248 CAU547_LH191_1 10951643 13937
## 307 SRR449249 CAU547_LH191_2 23289220 26716
## 308 SRR449264 CAU548_LH192_1 10372943 15657
## 309 SRR449267 CAU548_LH192_2 14068493 21263
## 310 SRR449268 CAU577_IB014_1 9392607 22613
## 311 SRR449269 CAU577_IB014_2 11433228 24608
## 312 SRR449271 CAU581_NS701_1 10179192 17466
## 313 SRR449273 CAU581_NS701_2 9626503 13581
## 314 SRR449274 CAU589_87916W_1 10859574 23350
## 315 SRR449276 CAU589_87916W_2 8537849 14971
## 316 SRR449277 CAU606_PHP60_1 10752774 15402
## 317 SRR449278 CAU606_PHP60_2 7504751 8147
## 318 SRR449338 CAU38_A632 54464972 190272
## 319 SRR449339 CAU38_A632 199389230 673164
## 320 SRR449340 CAU01_zheng58 209125666 407660
## 321 SRR449342 CAU01_zheng58 209580263 408759
## 322 SRR449343 CAU01_zheng58 208768794 405058
## 323 SRR449344 CAU02_chang7-2 215502743 831429
## 324 SRR449345 CAU02_chang7-2 218350980 839858
## 325 SRR449346 CAU02_chang7-2 219075959 844517
## 326 SRR449347 CAU05_478 202243498 348296
## 327 SRR449348 CAU05_478 205326838 354556
## 328 SRR449350 CAU06_zong31 71775570 264624
## 329 SRR449351 CAU07_D340 65873634 192562
## 330 SRR449352 CAU08_H127 62077760 79638
## 331 SRR449353 CAU04_5003 208710047 559023
## 332 SRR449354 CAU04_5003 206458795 550643
## 333 SRR449355 CAU04_5003 203394974 539144
## 334 SRR449357 CAU27_ye8112_1 72344710 159128
## 335 SRR449358 CAU27_ye8112_2 72138656 160106
## 336 SRR449359 CAU27_ye8112_2 72210648 159950
## 337 SRR449427 CAU196_ji846 56594786 161942
## 338 SRR449556 Mo17 58493122 196164
## 339 SRR449557 Mo17 76515600 251302
## 340 SRR449558 Mo17 84859352 282224
## 341 SRR528558 CAU27_ye8112_1 70447478 157124
## 342 SRR528559 CAU05_478 202711093 352427
## 343 SRR530830 CAU01_Zheng58_BGI_1 36928096 126734
## 344 SRR530831 CAU01_Zheng58_BGI_1 40903792 140124
## 345 SRR530833 CAU01_Zheng58_BGI_2 60876972 219422
## 346 SRR530834 CAU05_478_BGI_1 9272124 25056
## 347 SRR530835 CAU05_478_BGI_1 20982640 67612
## 348 SRR530836 CAU05_478_BGI_2 75322903 260699
## 349 SRR530837 CAU05_478_BGI_2 90188289 335429
## 350 SRR530838 CAU04_5003_BGI_1 55939904 259664
## 351 SRR530840 CAU04_5003_BGI_2 15798595 92253
## 352 SRR530841 CAU04_5003_BGI_2 18499082 109098
## 353 SRR671686 CAU223_H99 12430738 36060
## 354 SRR671687 CAU268_B8 12322367 49203
## 355 SRR671688 CAU272_M14 10879425 25687
## 356 SRR671689 CAU364_B7 9320574 25494
## 357 SRR671715 CAU427_H105W 14671771 51647
## 358 SRR671716 CAU532_PHG35 18012704 91024
## 359 SRR801200 CAU308_W117 7926228 31830
## 360 SRR801201 CAU421_CI66 6404880 18650
N = (x$Line)
x$Filename = NULL
fbyN = factor(N, exclude = " ")
x$Line = NULL
abun = aggregate(x, by = list(fbyN), FUN = "mean", na.rm = T)
abun2 = Filter(function(abun) !all(is.na(abun)), abun)
A = (abun2$Group.1)
B = (abun2$ReadsTotal)
C = (abun2$ReadsAligned)
## Percent reads mapped per lane
D = (abun2$ReadsAligned/abun2$ReadsTotal) * 100
abun3 = data.frame(A, B, C, D)
Columns
$A = Lines $B = Total_Reads $C = Reads_Mapped $D = Percent Abundance
print(abun3)
## A B C D
## 1 CAU01_zheng58 209158241 407159 0.1947
## 2 CAU01_Zheng58_BGI_1 38915944 133429 0.3429
## 3 CAU01_Zheng58_BGI_2 60876972 219422 0.3604
## 4 CAU02_chang7-2 217643227 838601 0.3853
## 5 CAU04_5003 206187939 549603 0.2666
## 6 CAU04_5003_BGI_1 55939904 259664 0.4642
## 7 CAU04_5003_BGI_2 17148838 100676 0.5871
## 8 CAU05_478 203427143 351760 0.1729
## 9 CAU05_478_BGI_1 15127382 46334 0.3063
## 10 CAU05_478_BGI_2 82755596 298064 0.3602
## 11 CAU06_zong31 70997878 262572 0.3698
## 12 CAU07_D340 66130164 194078 0.2935
## 13 CAU08_H127 62173306 80094 0.1288
## 14 CAU10_yu87-1 73665999 343879 0.4668
## 15 CAU100_shen5005 12737323 49179 0.3861
## 16 CAU103_807D 16300981 41193 0.2527
## 17 CAU105_1145 27641774 76810 0.2779
## 18 CAU107_D15 53675656 198572 0.3699
## 19 CAU11_longkang11 71102163 303269 0.4265
## 20 CAU112_S22 27845753 89273 0.3206
## 21 CAU114_Q1261 43456299 227633 0.5238
## 22 CAU115_ye52106 50490277 141159 0.2796
## 23 CAU116_1205A 54764200 170816 0.3119
## 24 CAU118_K12 66030692 252396 0.3822
## 25 CAU12_danhuang02 70336140 283288 0.4028
## 26 CAU120_xing230 37385244 109922 0.2940
## 27 CAU125_K22 29202964 110808 0.3794
## 28 CAU129_P007 24566122 77848 0.3169
## 29 CAU131_Yd6 39416761 149157 0.3784
## 30 CAU132_IA5125 34932498 104530 0.2992
## 31 CAU133_liao2202 11502078 31370 0.2727
## 32 CAU134_dai6 31280492 102582 0.3279
## 33 CAU137_W499 34393708 171602 0.4989
## 34 CAU14_shen137 47486913 106263 0.2238
## 35 CAU140_XOP2 44223532 184246 0.4166
## 36 CAU142_D20 38019353 121439 0.3194
## 37 CAU143_hai1134 42870887 177015 0.4129
## 38 CAU144_yu374 32233566 109602 0.3400
## 39 CAU146_dan9064 49369181 192125 0.3892
## 40 CAU147_niu2-1 13538012 47922 0.3540
## 41 CAU148_suwan1611 43960228 163656 0.3723
## 42 CAU149_R017 34030044 130890 0.3846
## 43 CAU15_zheng22 29773703 64439 0.2164
## 44 CAU151_shen977 19930255 78011 0.3914
## 45 CAU156_huangchangb 11487354 50438 0.4391
## 46 CAU16_lv28 57673105 138587 0.2403
## 47 CAU164_K10 19345929 47333 0.2447
## 48 CAU165_ye5237 24707450 74702 0.3023
## 49 CAU166_zheng32 52535130 148202 0.2821
## 50 CAU17_huangC 57497000 182706 0.3178
## 51 CAU173_P167 28674130 135954 0.4741
## 52 CAU174_R31 23611655 113447 0.4805
## 53 CAU178_changK 94898902 434250 0.4576
## 54 CAU18_P138 20583574 30762 0.1494
## 55 CAU180_M131-5 61677994 165462 0.2683
## 56 CAU19_zi330 20203713 23887 0.1182
## 57 CAU191_hai014 29485008 97956 0.3322
## 58 CAU192_ji444 32386915 101957 0.3148
## 59 CAU193_ben7884 26833842 94932 0.3538
## 60 CAU194_huangyesi3 54763986 176722 0.3227
## 61 CAU195_zaC546 26946562 46836 0.1738
## 62 CAU196_ji846 56594786 161942 0.2861
## 63 CAU197_4F1 54015843 326347 0.6042
## 64 CAU198_wenhuang31413 40507939 183209 0.4523
## 65 CAU199_ye515 28399048 151724 0.5343
## 66 CAU20_huangzaosi 191108428 471562 0.2468
## 67 CAU200_hu803 30856825 111139 0.3602
## 68 CAU201_tian77 25134401 80587 0.3206
## 69 CAU202_ye488 34013113 113031 0.3323
## 70 CAU203_chang72 34950611 113877 0.3258
## 71 CAU207_3H2 30424015 94969 0.3122
## 72 CAU208_cheng698-3 45204675 80377 0.1778
## 73 CAU21_tie7922 34600846 73624 0.2128
## 74 CAU210_su75 22677405 63865 0.2816
## 75 CAU211_Beck 24570811 64815 0.2638
## 76 CAU215_P136 21826556 84290 0.3862
## 77 CAU217_dan9046 110652778 277922 0.2512
## 78 CAU223_H99 12430738 36060 0.2901
## 79 CAU224_W64a 28249653 83065 0.2940
## 80 CAU225_A554 22544618 59010 0.2617
## 81 CAU229_xun92-8 25270525 99061 0.3920
## 82 CAU234_H21 8478073 21673 0.2556
## 83 CAU235_shuang741 8072594 23908 0.2962
## 84 CAU236_200B 15653412 81238 0.5190
## 85 CAU237_chong72 8337102 18500 0.2219
## 86 CAU238_Pa91 9208774 30586 0.3321
## 87 CAU239_yu537A 9160230 30154 0.3292
## 88 CAU24_9058 31221276 65416 0.2095
## 89 CAU242_dan3115 38457502 195070 0.5072
## 90 CAU244_zhonghuang64 37820345 130491 0.3450
## 91 CAU247_dong327 19962688 68990 0.3456
## 92 CAU248_698-3 32029684 80442 0.2511
## 93 CAU25_ji853 32829141 154575 0.4708
## 94 CAU251_N138 27867716 90582 0.3250
## 95 CAU254_DM07 22220776 50562 0.2275
## 96 CAU256_B100 14947591 40343 0.2699
## 97 CAU257_B98 60212549 268623 0.4461
## 98 CAU261_lian87 18753302 56758 0.3027
## 99 CAU264_L-1 23719370 49534 0.2088
## 100 CAU268_B8 12322367 49203 0.3993
## 101 CAU27_ye8112_1 71396094 158126 0.2215
## 102 CAU27_ye8112_2 72174652 160028 0.2217
## 103 CAU271_changD 40051432 187246 0.4675
## 104 CAU272_M14 10879425 25687 0.2361
## 105 CAU273_M101 29879889 75817 0.2537
## 106 CAU275_B394 24173114 68002 0.2813
## 107 CAU282_R25 20201814 55598 0.2752
## 108 CAU283_chengzi108 45166164 101062 0.2238
## 109 CAU289_ye107 24702858 51774 0.2096
## 110 CAU29_Maxa 23784872 71868 0.3022
## 111 CAU290_jiutai1 35612329 107623 0.3022
## 112 CAU294_hai9-21 24425785 65259 0.2672
## 113 CAU295_ji533 16621982 36380 0.2189
## 114 CAU297_ye832 11569584 14388 0.1244
## 115 CAU302_B76 11502697 41556 0.3613
## 116 CAU303_NC268 14851920 18758 0.1263
## 117 CAU306_Sg1533 10189651 22809 0.2238
## 118 CAU308_W117 7926228 31830 0.4016
## 119 CAU31_wu126 17207740 92194 0.5358
## 120 CAU310_7327 26323994 59452 0.2258
## 121 CAU316_bao3040 28374877 131595 0.4638
## 122 CAU320_Lx9801 8045818 42360 0.5265
## 123 CAU326_shen135 72490424 197866 0.2730
## 124 CAU33_yi36 19094166 63282 0.3314
## 125 CAU332_baihe43 18218361 54439 0.2988
## 126 CAU34_nan21-3 33345300 113218 0.3395
## 127 CAU345_jiu138-5 49171391 200959 0.4087
## 128 CAU347_ning55 29692827 80099 0.2698
## 129 CAU350_han21 28291355 74765 0.2643
## 130 CAU355_huotanghuang 33904579 122525 0.3614
## 131 CAU357_yu82 24306236 64534 0.2655
## 132 CAU359_CN165 20754591 57517 0.2771
## 133 CAU361_fu8701 20774876 49348 0.2375
## 134 CAU362_De811 15496102 38050 0.2455
## 135 CAU364_B7 9320574 25494 0.2735
## 136 CAU365_shan89 22904421 61139 0.2669
## 137 CAU366_A679 20135767 27335 0.1358
## 138 CAU367_Va26 18801218 49254 0.2620
## 139 CAU370_E28 15454342 35684 0.2309
## 140 CAU372_zhongyin15 13510250 38830 0.2874
## 141 CAU375_zong3 22163836 122318 0.5519
## 142 CAU38_A632 126927101 431718 0.3401
## 143 CAU382_FC-13 22841026 68706 0.3008
## 144 CAU384_ji63 10365432 31024 0.2993
## 145 CAU385_ji434 34082307 142149 0.4171
## 146 CAU386_ji4112 13385408 33715 0.2519
## 147 CAU389_qi205 14425716 31486 0.2183
## 148 CAU39_CM105 35389492 115096 0.3252
## 149 CAU40_B68 13638572 48226 0.3536
## 150 CAU400_P25 32415314 117880 0.3637
## 151 CAU401_R98 26702796 80880 0.3029
## 152 CAU402_qi319 13550726 28366 0.2093
## 153 CAU405_huo17 28841800 94224 0.3267
## 154 CAU409_huangyesi 37093956 120942 0.3260
## 155 CAU41_P39 21084501 86747 0.4114
## 156 CAU411_shen142 21734757 47355 0.2179
## 157 CAU413_siyi 19036920 34934 0.1835
## 158 CAU416_xun971 15462457 60265 0.3898
## 159 CAU42_shangyin110-1 31504085 107373 0.3408
## 160 CAU420_Mo24W 33120955 95843 0.2894
## 161 CAU421_CI66 6404880 18650 0.2912
## 162 CAU422_W182bn 26009306 99748 0.3835
## 163 CAU423_W153R 13300918 41608 0.3128
## 164 CAU425_HP301 12472032 22652 0.1816
## 165 CAU426_H84 17189062 52326 0.3044
## 166 CAU427_H105W 14671771 51647 0.3520
## 167 CAU429_tangsipingtou 38787828 90138 0.2324
## 168 CAU434_cheng18 49272940 169222 0.3434
## 169 CAU436_xinlun5-9 13084959 30095 0.2300
## 170 CAU439_lv45 19311211 82233 0.4258
## 171 CAU446_fengke1 16977653 53243 0.3136
## 172 CAU448_ernan24 51042513 139373 0.2731
## 173 CAU451_78371A 38269166 75738 0.1979
## 174 CAU452_PHT10 27149205 110831 0.4082
## 175 CAU453_PHH93 16415573 36245 0.2208
## 176 CAU454_IBB14 17226995 35829 0.2080
## 177 CAU458_LH149 14163820 24018 0.1696
## 178 CAU46_zhong451 23256779 88283 0.3796
## 179 CAU461_794 19284813 26345 0.1366
## 180 CAU463_PHR32 24228015 44805 0.1849
## 181 CAU465_PHG50 14695402 58534 0.3983
## 182 CAU466_LH51 24417690 48626 0.1991
## 183 CAU468_78010 24898674 85154 0.3420
## 184 CAU47_huotanghuang17 23972059 114844 0.4791
## 185 CAU470_LH39 47103161 97225 0.2064
## 186 CAU471_PHG84 19108803 43219 0.2262
## 187 CAU475_LH57 16830668 66678 0.3962
## 188 CAU476_LH38 16334952 57322 0.3509
## 189 CAU488_807 23807270 143235 0.6016
## 190 CAU489_OH43 34759023 80829 0.2325
## 191 CAU490_PHN11 27765047 68999 0.2485
## 192 CAU491_PHJ70 15360449 36073 0.2348
## 193 CAU492_DJ7 14545485 18975 0.1305
## 194 CAU496_790 15964608 26492 0.1659
## 195 CAU497_PHZ51 24078506 87564 0.3637
## 196 CAU498_PHT60 14620594 29412 0.2012
## 197 CAU501_PHG83 24887576 65110 0.2616
## 198 CAU503_PHJ75 24187584 38488 0.1591
## 199 CAU505_PB80 21949464 28734 0.1309
## 200 CAU510_LH52 13792096 79276 0.5748
## 201 CAU513_PHW52 14638728 35833 0.2448
## 202 CAU514_LH93 17886202 34698 0.1940
## 203 CAU515_PHM57 18103181 43457 0.2401
## 204 CAU517_LH60 11517747 22631 0.1965
## 205 CAU518_PHG71 13590704 16150 0.1188
## 206 CAU520_Q381 20250624 54980 0.2715
## 207 CAU521_MBPM 21247713 106011 0.4989
## 208 CAU522_PHW03 23367265 134176 0.5742
## 209 CAU523_PHW43 14786804 65312 0.4417
## 210 CAU525_LH190 19367353 32003 0.1652
## 211 CAU526_B47 16624648 36488 0.2195
## 212 CAU527_PHV78 33792310 105332 0.3117
## 213 CAU528 26704943 42697 0.1599
## 214 CAU530_PHK76 15586167 28763 0.1845
## 215 CAU531_LH1 28823487 63353 0.2198
## 216 CAU532_PHG35 18012704 91024 0.5053
## 217 CAU534_PHJ31 16875688 128760 0.7630
## 218 CAU535_78002A 12329211 18015 0.1461
## 219 CAU536_792 15532611 17591 0.1133
## 220 CAU537_PHJ40 14269066 26334 0.1846
## 221 CAU538_LH54 29737076 50808 0.1709
## 222 CAU539_FAPW 13815918 25404 0.1839
## 223 CAU541_LH205 16753999 81162 0.4844
## 224 CAU542_LH127 19107344 126898 0.6641
## 225 CAU545_LH194 16181938 56140 0.3469
## 226 CAU546_LH202 12749890 13538 0.1062
## 227 CAU547_LH191_1 10951643 13937 0.1273
## 228 CAU547_LH191_2 23289220 26716 0.1147
## 229 CAU548_LH192_1 10372943 15657 0.1509
## 230 CAU548_LH192_2 14068493 21263 0.1511
## 231 CAU549_RS710 21189070 90260 0.4260
## 232 CAU551_PHW51 18958238 144450 0.7619
## 233 CAU566_PHP85 21451287 87547 0.4081
## 234 CAU572_LH143 45251745 111625 0.2467
## 235 CAU574_207 32057836 88246 0.2753
## 236 CAU575_CR1HT 22266283 54949 0.2468
## 237 CAU576_6103 31176593 77119 0.2474
## 238 CAU577_IB014_1 9392607 22613 0.2408
## 239 CAU577_IB014_2 11433228 24608 0.2152
## 240 CAU578_4676A 22171802 48314 0.2179
## 241 CAU58_B12 55059522 241682 0.4389
## 242 CAU580_PHR36 15165187 35569 0.2345
## 243 CAU581_NS701_1 10179192 17466 0.1716
## 244 CAU581_NS701_2 9626503 13581 0.1411
## 245 CAU582_IB02 20362418 86736 0.4260
## 246 CAU583_IBB15 60631994 227658 0.3755
## 247 CAU584_787 23909393 81391 0.3404
## 248 CAU586_11430 31886535 106007 0.3325
## 249 CAU587_2369 21544298 49676 0.2306
## 250 CAU588_2MA22 17974364 62014 0.3450
## 251 CAU589_87916W_1 10859574 23350 0.2150
## 252 CAU589_87916W_2 8537849 14971 0.1753
## 253 CAU590_MBST 41341981 120985 0.2926
## 254 CAU591_PHN47 27884488 63528 0.2278
## 255 CAU592_NS501 19970813 37723 0.1889
## 256 CAU593_H8431 19612514 52832 0.2694
## 257 CAU594_S8324 22411308 36022 0.1607
## 258 CAU595_CR14 20019742 38858 0.1941
## 259 CAU596_WIL901 18022392 43180 0.2396
## 260 CAU597_WIL903 20377465 55931 0.2745
## 261 CAU598_WIL500 15765492 23848 0.1513
## 262 CAU599_E8501 27138560 59024 0.2175
## 263 CAU601_L135 16290430 31524 0.1935
## 264 CAU604_PHM10 21904476 66818 0.3050
## 265 CAU605_PHN82 26928798 91680 0.3405
## 266 CAU606_PHP60_1 10752774 15402 0.1432
## 267 CAU606_PHP60_2 7504751 8147 0.1086
## 268 CAU607_PHR63 27207431 100205 0.3683
## 269 CAU609_PHV37 39491933 195459 0.4949
## 270 CAU61_ji870 12808349 47745 0.3728
## 271 CAU610_PHW20 20836894 81654 0.3919
## 272 CAU611_W23 15964139 17655 0.1106
## 273 CAU63_fu8521 11713285 21948 0.1874
## 274 CAU631_PHP55 23777906 88620 0.3727
## 275 CAU638_huobai 36451636 75508 0.2071
## 276 CAU68_jiao05 39059217 143145 0.3665
## 277 CAU69_qi410 1353005 4707 0.3479
## 278 CAU73_xiangai3 67539877 237137 0.3511
## 279 CAU74_fusheA 49431847 279349 0.5651
## 280 CAU76_qiong51 56229192 162022 0.2881
## 281 CAU77_DH149 28236717 71201 0.2522
## 282 CAU78_R08 30134306 81824 0.2715
## 283 CAU84_B95 41561016 125696 0.3024
## 284 CAU97_guan17-1 13353754 47108 0.3528
## 285 CAU98_wu125 17059257 45377 0.2660
## 286 Mo17 73289358 243230 0.3319
write.table(abun3, "/Users/Sid/Projects/CRM_mapping/CRM_files/Jiao_CentC_abun.txt",
sep = "\t")
Statistical Summary
Stats for Percent Abundance
summary(D)
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.106 0.222 0.293 0.305 0.368 0.763
Average Abundance Across Lines
mean(D)
## [1] 0.3049
Plot showing Percent Reads Mapped per Lane.
hist(D, xlab = "Percent Reads Mapped", ylab = "Jiao Lines", col = rgb(0.4, 0.1,
0.3, 1/5), main = "CentC Abundance")