Experiments on SNPs' depth lower than 10

  • Author: Fang Zhang
  • Date: 2016.7.10
  • E-mail: fza34@sfu.ca

Experiment SNPs' depth

  1. After depth filter, 6925 SNPs in total including 4003 SNPs' frequency greater than 1. It is not relaible.

  2. The number and propotion of SNPs that have depth lower than10.

sample number_SNPs unresi propotion
ERR550643 92 1248 0.073717949
ERR550644 83 1263 0.065716548
ERR550658 103 1378 0.074746009
ERR550659 121 1446 0.083679115
ERR550670 51 1331 0.038317055
ERR550724 53 1491 0.035546613
ERR550738 66 1347 0.048997773
ERR550739 42 1415 0.029681979
ERR550777 172 1319 0.13040182
ERR550778 91 1347 0.067557535
ERR550779 727 1300 0.559230769
ERR550782 56 1404 0.03988604
ERR550783 90 1404 0.064102564
ERR550887 71 1383 0.051337672
ERR550910 24 1497 0.016032064
ERR550927 37 1345 0.027509294
ERR550940 63 1383 0.045553145
ERR550941 60 1331 0.045078888
ERR550946 42 1324 0.031722054
ERR550947 51 1309 0.038961039
ERR550957 54 1457 0.037062457
ERR550984 45 1397 0.032211883
ERR551007 24 1433 0.016748081
ERR551071 29 1397 0.020758769
ERR551079 57 1392 0.040948276
ERR551086 33 1360 0.024264706
ERR551090 55 1395 0.039426523
ERR551155 58 1355 0.042804428
ERR551156 69 1324 0.052114804
ERR551159 49 1433 0.034193999
ERR551167 62 1341 0.046234154
ERR551168 50 1368 0.036549708
ERR551184 56 1320 0.042424242
ERR551185 363 1244 0.291800643
ERR551201 34 1377 0.024691358
ERR551212 50 1399 0.035739814
ERR551214 79 1229 0.064279902
ERR551225 27 1384 0.019508671
ERR551293 36 1443 0.024948025
ERR551305 98 1398 0.070100143
ERR551311 48 1411 0.034018427
ERR551360 85 1399 0.060757684
ERR551361 141 1355 0.104059041
ERR551362 229 1339 0.171023152
ERR551369 65 1350 0.048148148
ERR551370 98 1336 0.073353293
ERR551412 73 1287 0.056721057
ERR551494 65 1422 0.045710267
ERR551520 23 1477 0.015572106
ERR551549 114 1498 0.076101469
ERR551554 43 1389 0.030957523
ERR551556 63 1376 0.045784884
ERR551557 500 1294 0.386398764
ERR551558 396 1308 0.302752294
ERR551572 45 1347 0.033407572
ERR551575 126 1197 0.105263158
ERR551636 51 1353 0.037694013
ERR551638 77 1379 0.055837563
ERR551680 47 1369 0.034331629
ERR551681 59 1337 0.044128646
ERR551688 71 1353 0.052475979
ERR551693 69 1344 0.051339286
ERR551694 67 1327 0.050489827
ERR551772 40 1473 0.027155465
ERR551804 93 1377 0.067538126
ERR551805 275 1328 0.207078313
ERR551806 347 1333 0.260315079
ERR551821 82 1405 0.058362989
ERR551822 88 1417 0.062103035
ERR551854 86 1298 0.066255778
ERR551855 70 1346 0.052005944
ERR551879 42 1398 0.030042918
ERR551927 91 1317 0.069096431
ERR551928 76 1341 0.056674124
ERR551930 55 1415 0.038869258
ERR551934 23 1481 0.015530047
ERR551943 829 1218 0.680623974
ERR551944 66 1354 0.048744461
ERR551945 48 1381 0.034757422
ERR551956 48 1367 0.035113387
ERR551957 47 1334 0.035232384
ERR551977 114 1314 0.086757991
ERR551978 58 1340 0.043283582
ERR551979 971 1103 0.880326383
ERR551980 585 1254 0.466507177
ERR551981 984 1187 0.828980623
ERR551982 183 1294 0.141421947
ERR551983 905 1026 0.882066277
ERR551990 30 1466 0.020463847
ERR552090 38 1469 0.025867937
ERR552130 35 1411 0.024805103
ERR552136 43 1405 0.030604982
ERR552141 48 1376 0.034883721
ERR552177 32 1383 0.023138106
ERR552190 26 1444 0.01800554
ERR552194 79 1429 0.055283415
ERR552219 60 1343 0.044676098
ERR552331 55 1388 0.03962536
ERR552358 37 1416 0.026129944
ERR552429 50 1406 0.035561878
ERR552444 54 1344 0.040178571
ERR552445 156 1286 0.121306376
ERR552479 60 1611 0.037243948
ERR552482 36 1436 0.025069638
ERR552493 69 1420 0.048591549
ERR552494 113 1415 0.079858657
ERR552549 55 1335 0.041198502
ERR552550 54 1318 0.040971168
ERR552555 41 1398 0.029327611
ERR552580 42 1401 0.029978587
ERR552668 116 1268 0.09148265
ERR552669 969 1227 0.789731051
ERR552670 432 1370 0.315328467
ERR552671 220 1372 0.160349854
ERR552689 67 1355 0.049446494
ERR552690 971 1158 0.83851468
ERR552743 43 1356 0.031710914
ERR552755 41 1337 0.030665669
ERR552760 48 1350 0.035555556
ERR552787 53 1391 0.038102085
ERR552830 64 1360 0.047058824
ERR552838 32 1376 0.023255814
ERR552894 62 1345 0.046096654
ERR552895 123 1288 0.095496894
ERR552907 66 1401 0.047109208
ERR552910 43 1384 0.031069364
ERR552911 68 1362 0.049926579
ERR552912 24 1419 0.016913319
ERR552939 98 1434 0.068340307
ERR552940 253 1487 0.170141224
ERR552949 82 1349 0.060785767
ERR552954 48 1383 0.034707158
ERR553068 48 1366 0.035139092
ERR553081 86 1338 0.064275037
ERR553082 53 1368 0.03874269
ERR553086 22 1463 0.015037594
ERR553098 55 1402 0.039229672
ERR553107 38 1372 0.027696793
ERR553116 53 1366 0.038799414
ERR553139 42 1406 0.029871977
ERR553156 50 1357 0.036845984
ERR553157 505 1306 0.386676876
ERR553171 36 1420 0.025352113
ERR553237 49 1392 0.035201149
ERR553251 38 1471 0.025832767
ERR553274 57 1312 0.043445122
ERR553275 113 1271 0.088906373
ERR553277 44 1382 0.031837916
ERR553291 46 1379 0.033357505
ERR553303 836 1272 0.657232704
ERR553304 95 1320 0.071969697
ERR553313 64 1390 0.046043165
ERR553324 36 1396 0.025787966
ERR619080 59 1398 0.042203147
  1. Many samples have a lot of SNPs that have depth lower than 10. We should check the fastq files first. mrFAST cannot work on fastq files that contain reads of different lengths. If reads are cut at 100, a lot information would be lost. Calculate top 2 long reads and the coverage. Almost at leat 1 sequence of one sample have low coverage. ERR551979-ERR551983 all have very low coverage. Thus we should delete these sequences. For those samples that have several high coverage sequences, we choose the higher one.
sample total_top2_1 total_1 second_top_length_1 propotion_1 average_depth_1 deleted total_top2_2 total_2 second_top_length_2 propotion_2 average_depth_2
ERR550643 352629 503810 250 0.69 20.04 1 365368 503810 250 0.72 20.76
ERR550659 457109 888025 150 0.51 15.58 1 459162 888025 150 0.51 15.65
ERR550777 366537 366537 151 1 12.58 1 366537 366537 151 1 12.58
ERR550779 175080 213152 150 0.82 5.97 1 175478 213152 150 0.82 5.98
ERR550783 301101 709644 250 0.42 17.11 1 329686 709644 250 0.46 18.73
ERR550940 816797 986163 150 0.82 27.85 1 816667 986163 150 0.82 27.84
ERR550946 847041 1062557 150 0.79 28.88 1 850563 1062557 150 0.8 29.00
ERR551155 657758 773602 250 0.85 37.37 1 681991 773602 250 0.88 38.75
ERR551168 730841 884768 150 0.82 24.92 1 732908 884768 150 0.82 24.99
ERR551185 201119 310721 250 0.64 11.43 1 205086 310721 250 0.66 11.65
ERR551361 301576 388916 250 0.77 17.14 1 311362 388916 250 0.8 17.69
ERR551362 272194 343012 150 0.79 9.28 1 272760 343012 150 0.79 9.30
ERR551370 560956 668918 250 0.83 31.87 1 525685 668918 250 0.78 29.87
ERR551557 193635 245514 250 0.78 11.00 1 199966 245514 250 0.81 11.36
ERR551558 228464 283281 150 0.8 7.79 1 228863 283281 150 0.8 7.80
ERR551681 450011 561151 250 0.8 25.57 1 466319 561151 250 0.83 26.50
ERR551694 555662 634595 250 0.87 31.57 1 523829 634595 250 0.82 29.76
ERR551805 242169 313777 250 0.77 13.76 1 250503 313777 250 0.79 14.23
ERR551806 238910 295816 150 0.8 8.14 1 238726 295816 150 0.8 8.14
ERR551822 498401 827650 150 0.6 16.99 1 500159 827650 150 0.6 17.05
ERR551854 367993 536581 250 0.68 20.91 1 376291 536581 250 0.7 21.38
ERR551927 371298 519638 250 0.71 21.10 1 377836 519638 250 0.72 21.47
ERR551943 166621 200229 150 0.83 5.68 1 166831 200229 150 0.83 5.69
ERR551945 764186 764186 151 1 26.23 1 764186 764186 151 1 26.23
ERR551957 520790 679521 250 0.76 29.59 1 544932 679521 250 0.8 30.96
ERR551977 345033 505726 250 0.68 19.60 1 354319 505726 250 0.7 20.13
ERR551979 73517 105647 250 0.69 4.18 1 73419 105647 250 0.69 4.17
ERR551980 190883 251974 150 0.75 6.51 1 190285 251974 150 0.75 6.49
ERR551981 78999 125109 300 0.63 5.39 1 78150 125109 300 0.62 5.33
ERR551982 389417 517259 150 0.75 13.28 1 385982 517259 150 0.74 13.16
ERR551983 64960 91448 250 0.71 3.69 1 65482 91448 250 0.71 3.72
ERR552445 293200 446898 250 0.65 16.66 1 301814 446898 250 0.67 17.15
ERR552494 263183 622615 250 0.42 14.95 1 283860 622615 250 0.45 16.13
ERR552549 623022 762902 250 0.81 35.40 1 647569 762902 250 0.84 36.79
ERR552669 55934 155915 250 0.35 3.18 1 69726 155915 250 0.44 3.96
ERR552670 184521 345974 150 0.53 6.29 1 183221 345974 150 0.52 6.25
ERR552671 489347 489347 151 1 16.79 1 489347 489347 151 1 16.79
ERR552690 89514 125815 250 0.71 5.09 1 91766 125815 250 0.72 5.21
ERR552895 471918 517150 250 0.91 26.81 1 484124 517150 250 0.93 27.51
ERR552911 478195 617093 250 0.77 27.17 1 502770 617093 250 0.81 28.57
ERR552940 261884 567079 150 0.46 8.93 1 263299 567079 150 0.46 8.98
ERR553081 466048 660126 250 0.7 26.48 1 501668 660126 250 0.75 28.50
ERR553157 185233 273412 250 0.67 10.52 1 190554 273412 250 0.69 10.83
ERR553275 397740 523197 250 0.76 22.60 1 418654 523197 250 0.8 23.79
ERR553303 159293 186850 250 0.85 9.05 1 170553 186850 250 0.91 9.69
ERR550644 368387 500989 250 0.73 20.93 390100 500989 250 0.77 22.16
ERR550658 694536 694536 151 1 23.84 694536 694536 151 1 23.84
ERR550670 942945 1067515 250 0.88 53.58 975660 1067515 250 0.91 55.44
ERR550724 4406794 4406794 51 1 51.08 4406794 4406794 51 1 51.08
ERR550738 664927 802441 250 0.82 37.78 618779 802441 250 0.77 35.16
ERR550739 1202191 1603567 150 0.74 40.98 1209489 1603567 150 0.75 41.23
ERR550778 403711 492341 250 0.81 22.94 417005 492341 250 0.84 23.69
ERR550782 1142598 1142598 151 1 39.21 1142598 1142598 151 1 39.21
ERR550887 681613 681613 150 1 23.24 681613 681613 150 1 23.24
ERR550910 6148758 6148758 101 1 141.14 6148758 6148758 101 1 141.14
ERR550927 895354 1126439 150 0.79 30.52 897513 1126439 150 0.79 30.60
ERR550941 528566 694478 250 0.76 30.03 553340 694478 250 0.79 31.44
ERR550947 560003 817328 250 0.68 31.82 593168 817328 250 0.72 33.70
ERR550957 2847379 2847379 101 1 65.36 2847379 2847379 101 1 65.36
ERR550984 1232580 1232580 151 1 42.30 1232580 1232580 151 1 42.30
ERR551007 3221955 3221955 101 1 73.96 3221955 3221955 101 1 73.96
ERR551071 1538003 2275846 150 0.67 52.43 1527328 2275846 150 0.67 52.07
ERR551079 831236 1153100 150 0.72 28.34 830923 1153100 150 0.72 28.33
ERR551086 1381621 1709345 150 0.8 47.10 1385599 1709345 150 0.81 47.24
ERR551090 912137 1125813 150 0.81 31.10 912726 1125813 150 0.81 31.12
ERR551156 667053 734670 250 0.9 37.90 686748 734670 250 0.93 39.02
ERR551159 1178805 1178805 151 1 40.45 1178805 1178805 151 1 40.45
ERR551167 746944 746944 151 1 25.63 746944 746944 151 1 25.63
ERR551184 639791 840348 150 0.76 21.81 639780 840348 150 0.76 21.81
ERR551201 1836130 1836130 151 1 63.01 1836130 1836130 151 1 63.01
ERR551212 1112021 1392359 150 0.79 37.91 1110539 1392359 150 0.79 37.86
ERR551214 2950693 2950693 72 1 48.28 2950693 2950693 72 1 48.28
ERR551225 2359668 2359668 101 1 54.17 2359668 2359668 101 1 54.17
ERR551293 3593886 3593886 100 1 81.68 3593886 3593886 100 1 81.68
ERR551305 649772 649772 150 1 22.15 649772 649772 150 1 22.15
ERR551311 920836 1595233 250 0.57 52.32 934011 1595233 250 0.58 53.07
ERR551360 531862 531862 151 1 18.25 531862 531862 151 1 18.25
ERR551369 634497 789026 250 0.8 36.05 664714 789026 250 0.84 37.77
ERR551412 501209 580388 250 0.86 28.48 510344 580388 250 0.87 29.00
ERR551494 997921 1252809 150 0.79 34.02 999254 1252809 150 0.79 34.07
ERR551520 7542333 7542333 101 1 173.13 7542333 7542333 101 1 173.13
ERR551549 3069058 3069058 101 1 70.45 3069058 3069058 101 1 70.45
ERR551554 1146272 1146272 151 1 39.34 1146272 1146272 151 1 39.34
ERR551556 557238 557238 151 1 19.12 557238 557238 151 1 19.12
ERR551572 966186 1156589 150 0.83 32.94 964154 1156589 150 0.83 32.87
ERR551575 2437684 2437684 72 1 39.89 2437684 2437684 72 1 39.89
ERR551636 905255 1116387 150 0.81 30.86 904961 1116387 150 0.81 30.85
ERR551638 696445 696445 150 1 23.74 696445 696445 150 1 23.74
ERR551680 856628 856628 151 1 29.40 856628 856628 151 1 29.40
ERR551688 714189 807272 250 0.88 40.58 741391 807272 250 0.91 42.12
ERR551693 617307 702723 250 0.87 35.07 636967 702723 250 0.9 36.19
ERR551772 4858274 4858274 51 1 56.31 4858274 4858274 51 1 56.31
ERR551804 528297 528297 151 1 18.13 528297 528297 151 1 18.13
ERR551821 751179 751179 151 1 25.78 751179 751179 151 1 25.78
ERR551855 549848 709020 250 0.77 31.24 574161 709020 250 0.8 32.62
ERR551879 1448715 1763371 150 0.82 49.39 1436155 1763371 150 0.81 48.96
ERR551928 485859 626266 250 0.77 27.61 507987 626266 250 0.81 28.86
ERR551930 1039805 1284539 150 0.8 35.45 1042954 1284539 150 0.81 35.56
ERR551934 4930930 4930930 101 1 113.19 4930930 4930930 101 1 113.19
ERR551944 626733 749579 250 0.83 35.61 646916 749579 250 0.86 36.76
ERR551956 1036490 1036490 151 1 35.57 1036490 1036490 151 1 35.57
ERR551978 579051 746633 250 0.77 32.90 610553 746633 250 0.81 34.69
ERR551990 2501148 2501148 101 1 57.41 2501148 2501148 101 1 57.41
ERR552090 3325371 3325371 100 1 75.58 3325371 3325371 100 1 75.58
ERR552130 1416680 1416680 151 1 48.62 1416680 1416680 151 1 48.62
ERR552136 1331643 1702445 150 0.78 45.40 1332191 1702445 150 0.78 45.42
ERR552141 775490 1344531 250 0.57 44.06 778789 1344531 250 0.57 44.25
ERR552177 2126018 2126018 101 1 48.80 2126018 2126018 101 1 48.80
ERR552190 2907157 2907157 101 1 66.73 2907157 2907157 101 1 66.73
ERR552194 833791 1147014 150 0.72 28.42 836118 1147014 150 0.72 28.50
ERR552219 772464 930462 250 0.83 43.89 723511 930462 250 0.77 41.11
ERR552331 1107102 1358539 150 0.81 37.74 1107211 1358539 150 0.81 37.75
ERR552358 1209857 1525080 150 0.79 41.25 1209470 1525080 150 0.79 41.23
ERR552429 1141376 1141376 151 1 39.17 1141376 1141376 151 1 39.17
ERR552444 688009 947208 150 0.72 23.45 686250 947208 150 0.72 23.39
ERR552479 19714536 19714536 51 1 228.51 19714536 19714536 51 1 228.51
ERR552482 1616551 2143831 150 0.75 55.11 1620080 2143831 150 0.75 55.23
ERR552493 1006307 1006307 151 1 34.53 1006307 1006307 151 1 34.53
ERR552550 635108 713215 250 0.89 36.09 657053 713215 250 0.92 37.33
ERR552555 1137494 1412348 150 0.8 38.78 1139900 1412348 150 0.8 38.86
ERR552580 1213962 1213962 151 1 41.66 1213962 1213962 151 1 41.66
ERR552668 480196 694259 250 0.69 27.28 555166 694259 250 0.79 31.54
ERR552689 771015 1014227 150 0.76 26.28 763536 1014227 150 0.75 26.03
ERR552743 874653 1227467 150 0.71 29.82 869799 1227467 150 0.7 29.65
ERR552755 932272 1145975 150 0.81 31.78 933642 1145975 150 0.81 31.83
ERR552760 916048 1122827 150 0.81 31.23 916825 1122827 150 0.81 31.26
ERR552787 1087121 1386109 150 0.78 37.06 1089473 1386109 150 0.78 37.14
ERR552830 703060 824463 250 0.85 39.95 661031 824463 250 0.8 37.56
ERR552838 1355502 1872386 150 0.72 46.21 1351777 1872386 150 0.72 46.08
ERR552894 573476 667626 250 0.85 32.58 592430 667626 250 0.88 33.66
ERR552907 849602 849602 150 1 28.96 849602 849602 150 1 28.96
ERR552910 909326 909326 151 1 31.21 909326 909326 151 1 31.21
ERR552912 3735481 3735481 101 1 85.75 3735481 3735481 101 1 85.75
ERR552939 942214 942214 151 1 32.34 942214 942214 151 1 32.34
ERR552949 565475 672440 250 0.84 32.13 531302 672440 250 0.79 30.19
ERR552954 1263899 1545167 150 0.81 43.09 1265777 1545167 150 0.81 43.15
ERR553068 952882 1037422 150 0.91 32.48 953885 1037422 150 0.91 32.52
ERR553082 843849 1039372 150 0.81 28.77 846859 1039372 150 0.81 28.87
ERR553086 4316346 4316346 101 1 99.08 4316346 4316346 101 1 99.08
ERR553098 1371902 1371902 150 1 46.77 1371902 1371902 150 1 46.77
ERR553107 1157028 1157028 151 1 39.71 1157028 1157028 151 1 39.71
ERR553116 639742 703989 150 0.9 21.81 639742 703989 150 0.9 21.81
ERR553139 1121756 1396599 150 0.8 38.24 1124357 1396599 150 0.8 38.33
ERR553156 604012 818966 150 0.73 20.59 600320 818966 150 0.73 20.47
ERR553171 1746795 1746795 101 1 40.10 1746795 1746795 101 1 40.10
ERR553237 921485 1137866 150 0.8 31.41 921637 1137866 150 0.8 31.42
ERR553251 4809482 4809482 51 1 55.75 4809482 4809482 51 1 55.75
ERR553274 726240 892990 150 0.81 24.76 727986 892990 150 0.81 24.82
ERR553277 907668 1203167 150 0.75 30.94 905914 1203167 150 0.75 30.88
ERR553291 892724 1083213 150 0.82 30.43 894784 1083213 150 0.82 30.50
ERR553304 513906 561524 250 0.91 29.20 527555 561524 250 0.93 29.97
ERR553313 1048464 1048464 151 1 35.98 1048464 1048464 151 1 35.98
ERR553324 1235342 1235342 151 1 42.39 1235342 1235342 151 1 42.39
ERR619080 669268 983056 300 0.68 45.63 718129 983056 300 0.73 48.96
  1. Samples should be deleted (45):
sample total_top2_1 total_1 second_top_length_1 propotion_1 average_depth_1 deleted total_top2_2 total_2 second_top_length_2 propotion_2 average_depth_2
ERR550643 352629 503810 250 0.69 20.04 1 365368 503810 250 0.72 20.76
ERR550659 457109 888025 150 0.51 15.58 1 459162 888025 150 0.51 15.65
ERR550777 366537 366537 151 1 12.58 1 366537 366537 151 1 12.58
ERR550779 175080 213152 150 0.82 5.97 1 175478 213152 150 0.82 5.98
ERR550783 301101 709644 250 0.42 17.11 1 329686 709644 250 0.46 18.73
ERR550940 816797 986163 150 0.82 27.85 1 816667 986163 150 0.82 27.84
ERR550946 847041 1062557 150 0.79 28.88 1 850563 1062557 150 0.8 29.00
ERR551155 657758 773602 250 0.85 37.37 1 681991 773602 250 0.88 38.75
ERR551168 730841 884768 150 0.82 24.92 1 732908 884768 150 0.82 24.99
ERR551185 201119 310721 250 0.64 11.43 1 205086 310721 250 0.66 11.65
ERR551361 301576 388916 250 0.77 17.14 1 311362 388916 250 0.8 17.69
ERR551362 272194 343012 150 0.79 9.28 1 272760 343012 150 0.79 9.30
ERR551370 560956 668918 250 0.83 31.87 1 525685 668918 250 0.78 29.87
ERR551557 193635 245514 250 0.78 11.00 1 199966 245514 250 0.81 11.36
ERR551558 228464 283281 150 0.8 7.79 1 228863 283281 150 0.8 7.80
ERR551681 450011 561151 250 0.8 25.57 1 466319 561151 250 0.83 26.50
ERR551694 555662 634595 250 0.87 31.57 1 523829 634595 250 0.82 29.76
ERR551805 242169 313777 250 0.77 13.76 1 250503 313777 250 0.79 14.23
ERR551806 238910 295816 150 0.8 8.14 1 238726 295816 150 0.8 8.14
ERR551822 498401 827650 150 0.6 16.99 1 500159 827650 150 0.6 17.05
ERR551854 367993 536581 250 0.68 20.91 1 376291 536581 250 0.7 21.38
ERR551927 371298 519638 250 0.71 21.10 1 377836 519638 250 0.72 21.47
ERR551943 166621 200229 150 0.83 5.68 1 166831 200229 150 0.83 5.69
ERR551945 764186 764186 151 1 26.23 1 764186 764186 151 1 26.23
ERR551957 520790 679521 250 0.76 29.59 1 544932 679521 250 0.8 30.96
ERR551977 345033 505726 250 0.68 19.60 1 354319 505726 250 0.7 20.13
ERR551979 73517 105647 250 0.69 4.18 1 73419 105647 250 0.69 4.17
ERR551980 190883 251974 150 0.75 6.51 1 190285 251974 150 0.75 6.49
ERR551981 78999 125109 300 0.63 5.39 1 78150 125109 300 0.62 5.33
ERR551982 389417 517259 150 0.75 13.28 1 385982 517259 150 0.74 13.16
ERR551983 64960 91448 250 0.71 3.69 1 65482 91448 250 0.71 3.72
ERR552445 293200 446898 250 0.65 16.66 1 301814 446898 250 0.67 17.15
ERR552494 263183 622615 250 0.42 14.95 1 283860 622615 250 0.45 16.13
ERR552549 623022 762902 250 0.81 35.40 1 647569 762902 250 0.84 36.79
ERR552669 55934 155915 250 0.35 3.18 1 69726 155915 250 0.44 3.96
ERR552670 184521 345974 150 0.53 6.29 1 183221 345974 150 0.52 6.25
ERR552671 489347 489347 151 1 16.79 1 489347 489347 151 1 16.79
ERR552690 89514 125815 250 0.71 5.09 1 91766 125815 250 0.72 5.21
ERR552895 471918 517150 250 0.91 26.81 1 484124 517150 250 0.93 27.51
ERR552911 478195 617093 250 0.77 27.17 1 502770 617093 250 0.81 28.57
ERR552940 261884 567079 150 0.46 8.93 1 263299 567079 150 0.46 8.98
ERR553081 466048 660126 250 0.7 26.48 1 501668 660126 250 0.75 28.50
ERR553157 185233 273412 250 0.67 10.52 1 190554 273412 250 0.69 10.83
ERR553275 397740 523197 250 0.76 22.60 1 418654 523197 250 0.8 23.79
ERR553303 159293 186850 250 0.85 9.05 1 170553 186850 250 0.91 9.69
  1. samples' reads length at 150 (36):
sample total_top2_1 total_1 second_top_length_1 propotion_1 average_depth_1 deleted total_top2_2 total_2 second_top_length_2 propotion_2 average_depth_2
ERR553068 952882 1037422 150 0.91 32.48 953885 1037422 150 0.91 32.52
ERR553116 639742 703989 150 0.9 21.81 639742 703989 150 0.9 21.81
ERR551572 966186 1156589 150 0.83 32.94 964154 1156589 150 0.83 32.87
ERR551879 1448715 1763371 150 0.82 49.39 1436155 1763371 150 0.81 48.96
ERR553291 892724 1083213 150 0.82 30.43 894784 1083213 150 0.82 30.50
ERR551090 912137 1125813 150 0.81 31.10 912726 1125813 150 0.81 31.12
ERR551636 905255 1116387 150 0.81 30.86 904961 1116387 150 0.81 30.85
ERR552331 1107102 1358539 150 0.81 37.74 1107211 1358539 150 0.81 37.75
ERR552755 932272 1145975 150 0.81 31.78 933642 1145975 150 0.81 31.83
ERR552760 916048 1122827 150 0.81 31.23 916825 1122827 150 0.81 31.26
ERR552954 1263899 1545167 150 0.81 43.09 1265777 1545167 150 0.81 43.15
ERR553082 843849 1039372 150 0.81 28.77 846859 1039372 150 0.81 28.87
ERR553274 726240 892990 150 0.81 24.76 727986 892990 150 0.81 24.82
ERR551086 1381621 1709345 150 0.8 47.10 1385599 1709345 150 0.81 47.24
ERR551930 1039805 1284539 150 0.8 35.45 1042954 1284539 150 0.81 35.56
ERR552555 1137494 1412348 150 0.8 38.78 1139900 1412348 150 0.8 38.86
ERR553139 1121756 1396599 150 0.8 38.24 1124357 1396599 150 0.8 38.33
ERR553237 921485 1137866 150 0.8 31.41 921637 1137866 150 0.8 31.42
ERR550927 895354 1126439 150 0.79 30.52 897513 1126439 150 0.79 30.60
ERR551212 1112021 1392359 150 0.79 37.91 1110539 1392359 150 0.79 37.86
ERR551494 997921 1252809 150 0.79 34.02 999254 1252809 150 0.79 34.07
ERR552358 1209857 1525080 150 0.79 41.25 1209470 1525080 150 0.79 41.23
ERR552136 1331643 1702445 150 0.78 45.40 1332191 1702445 150 0.78 45.42
ERR552787 1087121 1386109 150 0.78 37.06 1089473 1386109 150 0.78 37.14
ERR551184 639791 840348 150 0.76 21.81 639780 840348 150 0.76 21.81
ERR552689 771015 1014227 150 0.76 26.28 763536 1014227 150 0.75 26.03
ERR552482 1616551 2143831 150 0.75 55.11 1620080 2143831 150 0.75 55.23
ERR553277 907668 1203167 150 0.75 30.94 905914 1203167 150 0.75 30.88
ERR550739 1202191 1603567 150 0.74 40.98 1209489 1603567 150 0.75 41.23
ERR553156 604012 818966 150 0.73 20.59 600320 818966 150 0.73 20.47
ERR551079 831236 1153100 150 0.72 28.34 830923 1153100 150 0.72 28.33
ERR552194 833791 1147014 150 0.72 28.42 836118 1147014 150 0.72 28.50
ERR552444 688009 947208 150 0.72 23.45 686250 947208 150 0.72 23.39
ERR552838 1355502 1872386 150 0.72 46.21 1351777 1872386 150 0.72 46.08
ERR552743 874653 1227467 150 0.71 29.82 869799 1227467 150 0.7 29.65
ERR551071 1538003 2275846 150 0.67 52.43 1527328 2275846 150 0.67 52.07
  1. samples' reads length at 250 (24):
sample total_top2_1 total_1 second_top_length_1 propotion_1 average_depth_1 deleted total_top2_2 total_2 second_top_length_2 propotion_2 average_depth_2
ERR553304 513906 561524 250 0.91 29.20 527555 561524 250 0.93 29.97
ERR551156 667053 734670 250 0.9 37.90 686748 734670 250 0.93 39.02
ERR552550 635108 713215 250 0.89 36.09 657053 713215 250 0.92 37.33
ERR550670 942945 1067515 250 0.88 53.58 975660 1067515 250 0.91 55.44
ERR551688 714189 807272 250 0.88 40.58 741391 807272 250 0.91 42.12
ERR551693 617307 702723 250 0.87 35.07 636967 702723 250 0.9 36.19
ERR551412 501209 580388 250 0.86 28.48 510344 580388 250 0.87 29.00
ERR552830 703060 824463 250 0.85 39.95 661031 824463 250 0.8 37.56
ERR552894 573476 667626 250 0.85 32.58 592430 667626 250 0.88 33.66
ERR552949 565475 672440 250 0.84 32.13 531302 672440 250 0.79 30.19
ERR551944 626733 749579 250 0.83 35.61 646916 749579 250 0.86 36.76
ERR552219 772464 930462 250 0.83 43.89 723511 930462 250 0.77 41.11
ERR550738 664927 802441 250 0.82 37.78 618779 802441 250 0.77 35.16
ERR550778 403711 492341 250 0.81 22.94 417005 492341 250 0.84 23.69
ERR551369 634497 789026 250 0.8 36.05 664714 789026 250 0.84 37.77
ERR551855 549848 709020 250 0.77 31.24 574161 709020 250 0.8 32.62
ERR551928 485859 626266 250 0.77 27.61 507987 626266 250 0.81 28.86
ERR551978 579051 746633 250 0.77 32.90 610553 746633 250 0.81 34.69
ERR550941 528566 694478 250 0.76 30.03 553340 694478 250 0.79 31.44
ERR550644 368387 500989 250 0.73 20.93 390100 500989 250 0.77 22.16
ERR552668 480196 694259 250 0.69 27.28 555166 694259 250 0.79 31.54
ERR550947 560003 817328 250 0.68 31.82 593168 817328 250 0.72 33.70
ERR551311 920836 1595233 250 0.57 52.32 934011 1595233 250 0.58 53.07
ERR552141 775490 1344531 250 0.57 44.06 778789 1344531 250 0.57 44.25
  1. sample's reads length at 300 (1):
sample total_top2_1 total_1 second_top_length_1 propotion_1 average_depth_1 deleted total_top2_2 total_2 second_top_length_2 propotion_2 average_depth_2
ERR619080 669268 983056 300 0.68 45.63 718129 983056 300 0.73 48.96
  1. samples have uniform reads length (48):
sample total_top2_1 total_1 second_top_length_1 propotion_1 average_depth_1 deleted total_top2_2 total_2 second_top_length_2 propotion_2 average_depth_2
ERR550658 694536 694536 151 1 23.84 694536 694536 151 1 23.84
ERR550724 4406794 4406794 51 1 51.08 4406794 4406794 51 1 51.08
ERR550782 1142598 1142598 151 1 39.21 1142598 1142598 151 1 39.21
ERR550887 681613 681613 150 1 23.24 681613 681613 150 1 23.24
ERR550910 6148758 6148758 101 1 141.14 6148758 6148758 101 1 141.14
ERR550957 2847379 2847379 101 1 65.36 2847379 2847379 101 1 65.36
ERR550984 1232580 1232580 151 1 42.30 1232580 1232580 151 1 42.30
ERR551007 3221955 3221955 101 1 73.96 3221955 3221955 101 1 73.96
ERR551159 1178805 1178805 151 1 40.45 1178805 1178805 151 1 40.45
ERR551167 746944 746944 151 1 25.63 746944 746944 151 1 25.63
ERR551201 1836130 1836130 151 1 63.01 1836130 1836130 151 1 63.01
ERR551214 2950693 2950693 72 1 48.28 2950693 2950693 72 1 48.28
ERR551225 2359668 2359668 101 1 54.17 2359668 2359668 101 1 54.17
ERR551293 3593886 3593886 100 1 81.68 3593886 3593886 100 1 81.68
ERR551305 649772 649772 150 1 22.15 649772 649772 150 1 22.15
ERR551360 531862 531862 151 1 18.25 531862 531862 151 1 18.25
ERR551520 7542333 7542333 101 1 173.13 7542333 7542333 101 1 173.13
ERR551549 3069058 3069058 101 1 70.45 3069058 3069058 101 1 70.45
ERR551554 1146272 1146272 151 1 39.34 1146272 1146272 151 1 39.34
ERR551556 557238 557238 151 1 19.12 557238 557238 151 1 19.12
ERR551575 2437684 2437684 72 1 39.89 2437684 2437684 72 1 39.89
ERR551638 696445 696445 150 1 23.74 696445 696445 150 1 23.74
ERR551680 856628 856628 151 1 29.40 856628 856628 151 1 29.40
ERR551772 4858274 4858274 51 1 56.31 4858274 4858274 51 1 56.31
ERR551804 528297 528297 151 1 18.13 528297 528297 151 1 18.13
ERR551821 751179 751179 151 1 25.78 751179 751179 151 1 25.78
ERR551934 4930930 4930930 101 1 113.19 4930930 4930930 101 1 113.19
ERR551956 1036490 1036490 151 1 35.57 1036490 1036490 151 1 35.57
ERR551990 2501148 2501148 101 1 57.41 2501148 2501148 101 1 57.41
ERR552090 3325371 3325371 100 1 75.58 3325371 3325371 100 1 75.58
ERR552130 1416680 1416680 151 1 48.62 1416680 1416680 151 1 48.62
ERR552177 2126018 2126018 101 1 48.80 2126018 2126018 101 1 48.80
ERR552190 2907157 2907157 101 1 66.73 2907157 2907157 101 1 66.73
ERR552429 1141376 1141376 151 1 39.17 1141376 1141376 151 1 39.17
ERR552479 19714536 19714536 51 1 228.51 19714536 19714536 51 1 228.51
ERR552493 1006307 1006307 151 1 34.53 1006307 1006307 151 1 34.53
ERR552580 1213962 1213962 151 1 41.66 1213962 1213962 151 1 41.66
ERR552907 849602 849602 150 1 28.96 849602 849602 150 1 28.96
ERR552910 909326 909326 151 1 31.21 909326 909326 151 1 31.21
ERR552912 3735481 3735481 101 1 85.75 3735481 3735481 101 1 85.75
ERR552939 942214 942214 151 1 32.34 942214 942214 151 1 32.34
ERR553086 4316346 4316346 101 1 99.08 4316346 4316346 101 1 99.08
ERR553098 1371902 1371902 150 1 46.77 1371902 1371902 150 1 46.77
ERR553107 1157028 1157028 151 1 39.71 1157028 1157028 151 1 39.71
ERR553171 1746795 1746795 101 1 40.10 1746795 1746795 101 1 40.10
ERR553251 4809482 4809482 51 1 55.75 4809482 4809482 51 1 55.75
ERR553313 1048464 1048464 151 1 35.98 1048464 1048464 151 1 35.98
ERR553324 1235342 1235342 151 1 42.39 1235342 1235342 151 1 42.39
  1. SNPs of 89 samples.
sample reads length mapping error rate (%) GATK mpileup intersection resi unresi unrepeted repeted depth_unfiltered depth_filtered propotion
ERR552668 250 8 1100 2717 796 17 779 709 70 31 678 0.956276
ERR552949 250 8 997 2682 929 18 911 837 74 242 595 0.710872
ERR550738 250 8 1012 2456 929 13 916 839 77 309 530 0.631704
ERR552830 250 8 1090 2169 903 11 892 810 82 342 468 0.577778
ERR552219 250 8 1071 2023 893 13 880 804 76 441 363 0.451493
ERR553304 250 8 1518 2149 1258 22 1236 1102 134 837 265 0.240472
ERR552550 250 8 1398 2045 1195 18 1177 1062 115 867 195 0.183616
ERR551156 250 8 1473 2081 1246 21 1225 1078 147 884 194 0.179963
ERR551688 250 8 1492 2135 1243 17 1226 1086 140 897 189 0.174033
ERR551305 150 8 2006 4474 1637 24 1613 1382 231 1184 198 0.143271
ERR551638 150 8 1885 3946 1585 24 1561 1364 197 1192 172 0.1261
ERR550887 150 8 1916 3726 1598 25 1573 1352 221 1195 157 0.116124
ERR551549 101 4 2067 3140 1604 25 1579 1371 208 1224 147 0.107221
ERR552194 150 8 2076 3473 1624 23 1601 1362 239 1222 140 0.10279
ERR553274 150 8 1904 2324 1493 18 1475 1250 225 1139 111 0.0888
ERR553171 101 4 1830 5314 1540 18 1522 1307 215 1196 111 0.084927
ERR551167 151 8 1468 1494 1396 23 1373 1196 177 1097 99 0.082776
ERR552907 150 8 1843 3358 1548 24 1524 1304 220 1204 100 0.076687
ERR553116 150 8 2137 2290 1577 20 1557 1318 239 1218 100 0.075873
ERR550670 250 8 1543 1787 1259 22 1237 1082 155 1002 80 0.073937
ERR550957 101 4 1779 2088 1527 20 1507 1298 209 1211 87 0.067026
ERR551928 250 8 1925 1618 1467 19 1448 1266 182 1183 83 0.065561
ERR551412 250 8 1954 1637 1494 22 1472 1238 234 1158 80 0.06462
ERR551369 250 8 2017 1671 1508 19 1489 1295 194 1213 82 0.06332
ERR553313 151 8 1786 2053 1506 24 1482 1294 188 1213 81 0.062597
ERR551184 150 8 1730 1668 1447 17 1430 1189 241 1116 73 0.061396
ERR550941 250 8 1997 1662 1490 21 1469 1265 204 1189 76 0.060079
ERR552760 150 8 1994 2192 1517 18 1499 1253 246 1178 75 0.059856
ERR551693 250 8 2006 1665 1515 21 1494 1291 203 1215 76 0.058869
ERR553156 150 8 1742 1691 1463 18 1445 1244 201 1171 73 0.058682
ERR550778 250 8 1902 1661 1492 26 1466 1264 202 1190 74 0.058544
ERR550644 250 8 1771 1608 1398 18 1380 1196 184 1126 70 0.058528
ERR553098 150 8 1774 2777 1516 24 1492 1284 208 1209 75 0.058411
ERR551494 150 8 1949 2105 1559 23 1536 1305 231 1229 76 0.058238
ERR550658 151 8 1518 1512 1405 23 1382 1216 166 1148 68 0.055921
ERR551855 250 8 1826 1632 1452 19 1433 1250 183 1181 69 0.0552
ERR550947 250 8 1854 1591 1435 19 1416 1228 188 1161 67 0.05456
ERR551930 150 8 2007 2226 1597 19 1578 1322 256 1250 72 0.054463
ERR551821 151 8 1558 1554 1448 24 1424 1233 191 1166 67 0.054339
ERR552787 150 8 1939 2025 1519 19 1500 1276 224 1207 69 0.054075
ERR551311 250 8 2078 1674 1543 23 1520 1317 203 1248 69 0.052392
ERR552444 150 8 1784 1719 1483 17 1466 1229 237 1165 64 0.052075
ERR552755 150 8 1955 2065 1508 17 1491 1230 261 1166 64 0.052033
ERR551636 150 8 1941 2132 1495 18 1477 1243 234 1182 61 0.049075
ERR553291 150 8 1926 1988 1530 19 1511 1285 226 1223 62 0.048249
ERR552689 150 8 1763 1654 1449 20 1429 1223 206 1164 59 0.048242
ERR553082 150 8 1890 1971 1514 19 1495 1266 229 1205 61 0.048183
ERR552331 150 8 1924 1785 1511 19 1492 1268 224 1207 61 0.048107
ERR551090 150 8 1913 1867 1535 23 1512 1276 236 1215 61 0.047806
ERR552954 150 8 1900 1730 1527 22 1505 1285 220 1224 61 0.047471
ERR553068 150 8 2044 2027 1527 24 1503 1292 211 1231 61 0.047214
ERR551804 151 8 1595 1566 1465 24 1441 1235 206 1177 58 0.046964
ERR551360 151 8 1573 1559 1466 24 1442 1236 206 1178 58 0.046926
ERR550927 150 8 1971 2411 1516 18 1498 1250 248 1192 58 0.0464
ERR552177 101 4 1637 1907 1473 19 1454 1215 239 1159 56 0.046091
ERR551956 151 8 1598 1541 1451 24 1427 1216 211 1160 56 0.046053
ERR552894 250 8 1943 1611 1480 20 1460 1273 187 1216 57 0.044776
ERR551079 150 8 1880 1718 1512 19 1493 1267 226 1211 56 0.044199
ERR552141 250 8 1938 1655 1508 26 1482 1291 191 1234 57 0.044152
ERR553139 150 8 1925 2115 1579 23 1556 1296 260 1239 57 0.043981
ERR552136 150 8 1948 1802 1561 24 1537 1299 238 1242 57 0.04388
ERR551978 250 8 1829 1584 1423 18 1405 1235 170 1181 54 0.043725
ERR552939 151 8 1547 1563 1433 23 1410 1211 199 1159 52 0.04294
ERR550782 151 8 1592 1564 1471 23 1448 1239 209 1186 53 0.042776
ERR551212 150 8 1920 1877 1540 24 1516 1297 219 1242 55 0.042406
ERR551201 151 8 1590 1534 1452 19 1433 1235 198 1183 52 0.042105
ERR552090 100 4 1673 1765 1536 22 1514 1288 226 1234 54 0.041925
ERR553277 150 8 1945 1741 1528 20 1508 1265 243 1212 53 0.041897
ERR619080 300 6.6 2020 1694 1551 19 1532 1301 231 1247 54 0.041507
ERR552910 151 8 1569 1521 1446 22 1424 1242 182 1192 50 0.040258
ERR551944 250 8 2028 1717 1543 23 1520 1295 225 1243 52 0.040154
ERR552429 151 8 1607 1585 1486 26 1460 1250 210 1200 50 0.04
ERR552555 150 8 1977 2054 1557 21 1536 1279 257 1228 51 0.039875
ERR553237 150 8 1962 1895 1542 22 1520 1285 235 1234 51 0.039689
ERR552743 150 8 1792 1687 1484 19 1465 1246 219 1197 49 0.039326
ERR551086 150 8 1908 1937 1541 18 1523 1248 275 1199 49 0.039263
ERR551990 101 4 1721 1865 1550 19 1531 1281 250 1232 49 0.038251
ERR551680 151 8 1589 1546 1467 20 1447 1240 207 1193 47 0.037903
ERR551556 151 8 1590 1519 1441 24 1417 1228 189 1182 46 0.037459
ERR550984 151 8 1578 1531 1455 22 1433 1241 192 1195 46 0.037067
ERR551225 101 4 1642 1750 1466 18 1448 1195 253 1151 44 0.03682
ERR552482 150 8 1962 2123 1592 25 1567 1305 262 1257 48 0.036782
ERR551554 151 8 1570 1555 1464 23 1441 1251 190 1205 46 0.036771
ERR552130 151 8 1604 1550 1456 20 1436 1225 211 1180 45 0.036735
ERR551879 150 8 1927 1772 1543 19 1524 1272 252 1226 46 0.036164
ERR551572 150 8 1856 1737 1498 18 1480 1228 252 1184 44 0.035831
ERR552493 151 8 1595 1570 1473 21 1452 1230 222 1187 43 0.034959
ERR552190 101 4 1660 1735 1506 19 1487 1269 218 1225 44 0.034673
ERR553107 151 8 1556 1518 1434 24 1410 1192 218 1151 41 0.034396
ERR552358 150 8 2025 1908 1559 24 1535 1285 250 1241 44 0.034241
ERR553324 151 8 1574 1535 1458 19 1439 1246 193 1204 42 0.033708
ERR551159 151 8 1615 1576 1475 22 1453 1252 201 1210 42 0.033546
ERR552580 151 8 1604 1561 1479 25 1454 1257 197 1215 42 0.033413
ERR550739 150 8 1859 1750 1544 19 1525 1273 252 1233 40 0.031422
ERR551293 100 4 1635 1737 1502 20 1482 1249 233 1210 39 0.031225
ERR552912 101 4 1634 1780 1491 18 1473 1212 261 1175 37 0.030528
ERR553086 101 4 1688 1764 1531 19 1512 1254 258 1216 38 0.030303
ERR552838 150 8 1821 1696 1517 19 1498 1224 274 1187 37 0.030229
ERR551071 150 8 1873 1701 1522 20 1502 1266 236 1228 38 0.030016
ERR551934 101 4 1695 1722 1545 19 1526 1263 263 1226 37 0.029295
ERR551007 101 4 1648 1720 1498 19 1479 1254 225 1218 36 0.028708
ERR550910 101 4 1720 1689 1562 19 1543 1284 259 1252 32 0.024922
ERR551520 101 4 1681 1665 1534 19 1515 1280 235 1251 29 0.022656
  1. SNP frequency. (6336 in total, 2705 occur more than once.)

  2. SNPs of 103 samples using error rate 4%.

sample reads length GATK mpileup intersection resi unresi unrepeted repeted depth_unfiltered depth_filtered propotion deleted
ERR550738 250 0 0 #DIV/0! 1
ERR552219 250 1 1 1 1 1 0 1 1 1
ERR552668 250 98 117 84 1 83 78 5 78 1 1
ERR552830 250 3 3 3 3 2 1 2 1 1
ERR552949 250 1 2 1 1 1 0 1 1 1
ERR553304 250 1103 1437 988 18 970 895 75 48 847 0.946368715 1
ERR551156 250 1131 1563 1033 19 1014 936 78 96 840 0.897435897 1
ERR551688 250 1145 1565 1051 16 1035 953 82 101 852 0.894018888 1
ERR552550 250 1111 1560 987 13 974 908 66 103 805 0.886563877 1
ERR550670 250 1214 1667 1120 20 1100 1014 86 265 749 0.738658777 1
ERR551305 150 2006 4474 1637 24 1613 1382 231 1184 198 0.143270622 1
ERR551638 150 1885 3946 1585 24 1561 1364 197 1192 172 0.126099707 1
ERR552194 150 1748 3551 1563 23 1540 1340 200 1181 159 0.118656716 1
ERR550887 150 1916 3726 1598 25 1573 1352 221 1195 157 0.11612426 1
ERR551549 101 2067 3140 1604 25 1579 1371 208 1224 147 0.107221007 1
ERR553171 101 1830 5314 1540 18 1522 1307 215 1196 111 0.084927314
ERR550941 250 1667 1565 1429 21 1408 1234 174 1130 104 0.084278768
ERR551167 151 1468 1494 1396 23 1373 1196 177 1097 99 0.08277592
ERR553274 150 1591 2266 1401 18 1383 1205 178 1106 99 0.082157676
ERR550644 250 1516 1513 1347 18 1329 1175 154 1080 95 0.080851064
ERR551978 250 1557 1491 1382 19 1363 1215 148 1117 98 0.080658436
ERR553116 150 1720 2098 1496 20 1476 1284 192 1181 103 0.080218069
ERR553156 150 1506 1634 1404 19 1385 1227 158 1130 97 0.079054605
ERR551855 250 1580 1503 1405 19 1386 1233 153 1136 97 0.078669911
ERR552907 150 1843 3358 1548 24 1524 1304 220 1204 100 0.076687117
ERR551184 150 1490 1604 1374 18 1356 1165 191 1081 84 0.072103004
ERR550947 250 1562 1478 1378 20 1358 1200 158 1118 82 0.068333333
ERR550957 101 1779 2088 1527 20 1507 1298 209 1211 87 0.067026194
ERR552141 250 1647 1537 1450 26 1424 1256 168 1173 83 0.066082803
ERR550778 250 1617 1592 1433 26 1407 1236 171 1156 80 0.064724919
ERR552689 150 1494 1562 1376 20 1356 1196 160 1121 75 0.06270903
ERR553313 151 1786 2053 1506 24 1482 1294 188 1213 81 0.0625966
ERR550927 150 1642 2397 1444 17 1427 1227 200 1154 73 0.059494703
ERR551928 250 1641 1533 1416 20 1396 1227 169 1154 73 0.059494703
ERR551930 150 1648 2204 1490 19 1471 1274 197 1199 75 0.058869702
ERR553082 150 1577 1903 1442 19 1423 1246 177 1173 73 0.05858748
ERR553098 150 1774 2777 1516 24 1492 1284 208 1209 75 0.058411215
ERR551412 250 1574 1520 1388 23 1365 1194 171 1125 69 0.057788945
ERR552760 150 1640 2177 1439 18 1421 1214 207 1144 70 0.057660626
ERR552755 150 1618 2019 1429 17 1412 1201 211 1133 68 0.056619484
ERR553237 150 1636 1819 1471 22 1449 1259 190 1188 71 0.056393963
ERR550658 151 1518 1512 1405 23 1382 1216 166 1148 68 0.055921053
ERR552444 150 1490 1652 1391 17 1374 1182 192 1116 66 0.055837563
ERR551636 150 1633 2103 1418 18 1400 1210 190 1143 67 0.055371901
ERR551369 250 1685 1531 1433 19 1414 1250 164 1181 69 0.0552
ERR552743 150 1558 1592 1410 19 1391 1224 167 1157 67 0.054738562
ERR551944 250 1675 1565 1457 23 1434 1249 185 1181 68 0.054443555
ERR551821 151 1558 1554 1448 24 1424 1233 191 1166 67 0.054339011
ERR551693 250 1661 1515 1442 22 1420 1243 177 1176 67 0.05390185
ERR553068 150 1692 1833 1472 24 1448 1261 187 1194 67 0.053132435
ERR552894 250 1632 1505 1418 20 1398 1236 162 1171 65 0.052588997
ERR552954 150 1594 1612 1435 22 1413 1244 169 1179 65 0.052250804
ERR551079 150 1572 1598 1427 19 1408 1237 171 1175 62 0.050121261
ERR553291 150 1603 1913 1449 19 1430 1247 183 1185 62 0.049719326
ERR551494 150 1636 2035 1475 23 1452 1260 192 1200 60 0.047619048
ERR553277 150 1613 1620 1443 20 1423 1232 191 1174 58 0.047077922
ERR551804 151 1595 1566 1465 24 1441 1235 206 1177 58 0.046963563
ERR551360 151 1573 1559 1466 24 1442 1236 206 1178 58 0.046925566
ERR551212 150 1599 1743 1454 24 1430 1258 172 1199 59 0.046899841
ERR551311 250 1707 1544 1453 23 1430 1257 173 1199 58 0.046141607
ERR551086 150 1619 1868 1445 18 1427 1214 213 1158 56 0.046128501
ERR552177 101 1637 1907 1473 19 1454 1215 239 1159 56 0.046090535
ERR551956 151 1598 1541 1451 24 1427 1216 211 1160 56 0.046052632
ERR552787 150 1626 1933 1445 19 1426 1233 193 1177 56 0.04541768
ERR550739 150 1563 1612 1465 19 1446 1245 201 1189 56 0.04497992
ERR551090 150 1576 1769 1439 23 1416 1237 179 1183 54 0.043654002
ERR552555 150 1653 1981 1469 21 1448 1242 206 1188 54 0.043478261
ERR551572 150 1600 1600 1424 18 1406 1200 206 1148 52 0.043333333
ERR552939 151 1547 1563 1433 23 1410 1211 199 1159 52 0.042939719
ERR550782 151 1592 1564 1471 23 1448 1239 209 1186 53 0.042776433
ERR551201 151 1590 1534 1452 19 1433 1235 198 1183 52 0.042105263
ERR552136 150 1615 1667 1466 24 1442 1261 181 1208 53 0.042030135
ERR552090 100 1673 1765 1536 22 1514 1288 226 1234 54 0.041925466
ERR551879 150 1633 1601 1459 19 1440 1245 195 1194 51 0.040963855
ERR552331 150 1646 1687 1438 19 1419 1229 190 1179 50 0.040683483
ERR553139 150 1663 2085 1490 23 1467 1257 210 1206 51 0.040572792
ERR552910 151 1569 1521 1446 22 1424 1242 182 1192 50 0.040257649
ERR552429 151 1607 1585 1486 26 1460 1250 210 1200 50 0.04
ERR552358 150 1607 1793 1468 24 1444 1254 190 1204 50 0.039872408
ERR619080 300 1757 1612 1501 19 1482 1265 217 1215 50 0.039525692
ERR551990 101 1721 1865 1550 19 1531 1281 250 1232 49 0.038251366
ERR552482 150 1669 2075 1500 25 1475 1259 216 1211 48 0.038125496
ERR551680 151 1589 1546 1467 20 1447 1240 207 1193 47 0.037903226
ERR551556 151 1590 1519 1441 24 1417 1228 189 1182 46 0.037459283
ERR550984 151 1578 1531 1455 22 1433 1241 192 1195 46 0.037066882
ERR551225 101 1642 1750 1466 18 1448 1195 253 1151 44 0.036820084
ERR551554 151 1570 1555 1464 23 1441 1251 190 1205 46 0.036770584
ERR552130 151 1604 1550 1456 20 1436 1225 211 1180 45 0.036734694
ERR552838 150 1549 1558 1417 19 1398 1191 207 1149 42 0.035264484
ERR552493 151 1595 1570 1473 21 1452 1230 222 1187 43 0.03495935
ERR552190 101 1660 1735 1506 19 1487 1269 218 1225 44 0.034672971
ERR553107 151 1556 1518 1434 24 1410 1192 218 1151 41 0.034395973
ERR553324 151 1574 1535 1458 19 1439 1246 193 1204 42 0.033707865
ERR551159 151 1615 1576 1475 22 1453 1252 201 1210 42 0.033546326
ERR552580 151 1604 1561 1479 25 1454 1257 197 1215 42 0.033412888
ERR551071 150 1563 1549 1436 20 1416 1228 188 1189 39 0.031758958
ERR551293 100 1635 1737 1502 20 1482 1249 233 1210 39 0.03122498
ERR552912 101 1634 1780 1491 18 1473 1212 261 1175 37 0.030528053
ERR553086 101 1688 1764 1531 19 1512 1254 258 1216 38 0.03030303
ERR551934 101 1695 1722 1545 19 1526 1263 263 1226 37 0.029295329
ERR551007 101 1648 1720 1498 19 1479 1254 225 1218 36 0.028708134
ERR550910 101 1720 1689 1562 19 1543 1284 259 1252 32 0.024922118
ERR551520 101 1681 1665 1534 19 1515 1280 235 1251 29 0.02265625
  1. SNP frequency. (6233 in total, 2539 occur more than once.)

  2. SNPs of 104 samples (combine multi-sequenced samples) using error rate 4%. 6403 SNPs in total.

sample reads length GATK mpileup intersection resi unresi unrepeted repeted depth_unfiltered depth_filtered propotion deleted total_reads mapped_reads propotion
ERR550670 250 1214 1667 1120 20 1100 1014 86 265 749 0.738658777 1 0
ERR550738 250 0 0 #DIV/0! 1 0
ERR550887 150 1916 3726 1598 25 1573 1352 221 1195 157 0.11612426 1 0
ERR551305 150 2006 4474 1637 24 1613 1382 231 1184 198 0.143270622 1 0
ERR551549 101 2067 3140 1604 25 1579 1371 208 1224 147 0.107221007 1 0
ERR551638 150 1885 3946 1585 24 1561 1364 197 1192 172 0.126099707 1 0
ERR551688 250 1145 1565 1051 16 1035 953 82 101 852 0.894018888 1 0
ERR551892 150 1584 1886 1396 19 1377 1207 170 1019 188 0.155758078 1 0
ERR552194 150 1748 3551 1563 23 1540 1340 200 1181 159 0.118656716 1 0
ERR552219 250 1 1 1 1 1 0 1 1 1 0
ERR552668 250 1400 1930 1289 19 1270 1156 114 59 1097 0.948961938 1 0
ERR552830 250 3 3 3 3 2 1 2 1 1 0
ERR552949 250 1 2 1 1 1 0 1 1 1 0
ERR553304 250 1459 1667 1330 24 1306 1160 146 618 542 0.467241379 1 0
ERR552550 250 1620 1502 1420 20 1400 1235 165 1174 61 0.049392713 2396642 1357790 0.566539
ERR551156 250 1636 1519 1445 23 1422 1248 174 1172 76 0.060897436 2533326 1465744 0.578585
ERR551293 100 1635 1737 1502 20 1482 1249 233 1210 39 0.03122498 4736584 2897215 0.611668
ERR551167 151 1532 1531 1442 24 1418 1227 191 1177 50 0.040749796 2609952 2213025 0.847918
ERR551978 250 1605 1487 1408 19 1389 1230 159 1158 72 0.058536585 1689220 1354323 0.801745
ERR551855 250 1629 1506 1426 19 1407 1246 161 1163 83 0.066613162 1672044 1359999 0.813375
ERR552141 250 1647 1537 1450 26 1424 1256 168 1173 83 0.066082803 1298916 1133219 0.872434
ERR551369 250 1685 1531 1433 19 1414 1250 164 1181 69 0.0552 1216086 1076319 0.885068
ERR550927 150 1642 2397 1444 17 1427 1227 200 1154 73 0.059494703 912228 813745 0.892041
ERR550941 250 1667 1565 1429 21 1408 1234 174 1130 104 0.084278768 991408 885211 0.892883
ERR550947 250 1562 1478 1378 20 1358 1200 158 1118 82 0.068333333 1040720 929919 0.893534
ERR552894 250 1632 1505 1418 20 1398 1236 162 1171 65 0.052588997 1100050 984405 0.894873
ERR551693 250 1661 1515 1442 22 1420 1243 177 1176 67 0.05390185 1186480 1071011 0.902679
ERR550644 250 1516 1513 1347 18 1329 1175 154 1080 95 0.080851064 698066 638463 0.914617
ERR551412 250 1574 1520 1388 23 1365 1194 171 1125 69 0.057788945 946542 882508 0.93235
ERR552689 150 1494 1562 1376 20 1356 1196 160 1121 75 0.06270903 1305814 1220508 0.934672
ERR551311 250 1707 1544 1453 23 1430 1257 173 1199 58 0.046141607 1571140 1495360 0.951768
ERR550957 101 1779 2088 1527 20 1507 1298 209 1211 87 0.067026194 5688770 5419416 0.952652
ERR551071 150 1563 1549 1436 20 1416 1228 188 1189 39 0.031758958 2609908 2491248 0.954535
ERR552910 151 1569 1521 1446 22 1424 1242 182 1192 50 0.040257649 1707738 1632389 0.955878
ERR552130 151 1604 1550 1456 20 1436 1225 211 1180 45 0.036734694 2587326 2473775 0.956113
ERR551184 150 1490 1604 1374 18 1356 1165 191 1081 84 0.072103004 1089680 1042094 0.95633
ERR551879 150 1633 1601 1459 19 1440 1245 195 1194 51 0.040963855 2455200 2349251 0.956847
ERR551554 151 1570 1555 1464 23 1441 1251 190 1205 46 0.036770584 2128132 2038519 0.957891
ERR550778 250 1617 1592 1433 26 1407 1236 171 1156 80 0.064724919 768996 737139 0.958573
ERR553171 101 1830 5314 1540 18 1522 1307 215 1196 111 0.084927314 3490754 3350274 0.959757
ERR553156 150 1506 1634 1404 19 1385 1227 158 1130 97 0.079054605 1026854 986525 0.960726
ERR553324 151 1574 1535 1458 19 1439 1246 193 1204 42 0.033707865 2279068 2202337 0.966332
ERR552444 150 1490 1652 1391 17 1374 1182 192 1116 66 0.055837563 1170018 1131219 0.966839
ERR552743 150 1558 1592 1410 19 1391 1224 167 1157 67 0.054738562 1488232 1441487 0.96859
ERR551944 250 1675 1565 1457 23 1434 1249 185 1181 68 0.054443555 1194088 1159478 0.971016
ERR552838 150 1549 1558 1417 19 1398 1191 207 1149 42 0.035264484 2304516 2241974 0.972861
ERR619080 300 1757 1612 1501 19 1482 1265 217 1215 50 0.039525692 1276754 1242556 0.973215
ERR552755 150 1618 2019 1429 17 1412 1201 211 1133 68 0.056619484 1586098 1563844 0.985969
ERR551636 150 1633 2103 1418 18 1400 1210 190 1143 67 0.055371901 1554552 1541447 0.99157
ERR551201 151 1590 1534 1452 19 1433 1235 198 1183 52 0.042105263 1882986 1867816 0.991944
ERR550739 150 1563 1612 1465 19 1446 1245 201 1189 56 0.04497992 2062790 2057266 0.997322
ERR553277 150 1613 1620 1443 20 1423 1232 191 1174 58 0.047077922 1558832 1555926 0.998136
ERR552760 150 1640 2177 1439 18 1421 1214 207 1144 70 0.057660626 1575228 1574607 0.999606
ERR551572 150 1600 1600 1424 18 1406 1200 206 1148 52 0.043333333 1655372 1658634 1.001971
ERR551956 151 1598 1541 1451 24 1427 1216 211 1160 56 0.046052632 1937780 1946675 1.00459
ERR553274 150 1591 2266 1401 18 1383 1205 178 1106 99 0.082157676 1240566 1255259 1.011844
ERR551079 150 1572 1598 1427 19 1408 1237 171 1175 62 0.050121261 1428506 1448239 1.013814
ERR551821 151 1558 1554 1448 24 1424 1233 191 1166 67 0.054339011 1046466 1061690 1.014548
ERR550984 151 1578 1531 1455 22 1433 1241 192 1195 46 0.037066882 1890834 1924620 1.017868
ERR550658 151 1518 1512 1405 23 1382 1216 166 1148 68 0.055921053 863140 879385 1.018821
ERR552177 101 1637 1907 1473 19 1454 1215 239 1159 56 0.046090535 4243410 4325673 1.019386
ERR551159 151 1615 1576 1475 22 1453 1252 201 1210 42 0.033546326 2184496 2228021 1.019925
ERR552787 150 1626 1933 1445 19 1426 1233 193 1177 56 0.04541768 1858836 1897547 1.020825
ERR552429 151 1607 1585 1486 26 1460 1250 210 1200 50 0.04 2138840 2187578 1.022787
ERR551928 250 1641 1533 1416 20 1396 1227 169 1154 73 0.059494703 1540416 1575697 1.022904
ERR552358 150 1607 1793 1468 24 1444 1254 190 1204 50 0.039872408 2074686 2124352 1.023939
ERR552907 150 1843 3358 1548 24 1524 1304 220 1204 100 0.076687117 1696604 1737404 1.024048
ERR552136 150 1615 1667 1466 24 1442 1261 181 1208 53 0.042030135 2283730 2339834 1.024567
ERR551086 150 1619 1868 1445 18 1427 1214 213 1158 56 0.046128501 2356740 2414651 1.024573
ERR550782 151 1592 1564 1471 23 1448 1239 209 1186 53 0.042776433 1663660 1704847 1.024757
ERR552939 151 1547 1563 1433 23 1410 1211 199 1159 52 0.042939719 1039346 1065337 1.025007
ERR551494 150 1636 2035 1475 23 1452 1260 192 1200 60 0.047619048 1695738 1738414 1.025167
ERR551680 151 1589 1546 1467 20 1447 1240 207 1193 47 0.037903226 1619014 1660271 1.025483
ERR553107 151 1556 1518 1434 24 1410 1192 218 1151 41 0.034395973 2154118 2210031 1.025956
ERR553237 150 1636 1819 1471 22 1449 1259 190 1188 71 0.056393963 1574448 1616065 1.026433
ERR552580 151 1604 1561 1479 25 1454 1257 197 1215 42 0.033412888 2216172 2275218 1.026643
ERR552954 150 1594 1612 1435 22 1413 1244 169 1179 65 0.052250804 2161554 2221847 1.027893
ERR551212 150 1599 1743 1454 24 1430 1258 172 1199 59 0.046899841 1903672 1959041 1.029085
ERR552493 151 1595 1570 1473 21 1452 1230 222 1187 43 0.03495935 1419088 1462726 1.030751
ERR553082 150 1577 1903 1442 19 1423 1246 177 1173 73 0.05858748 1437966 1484797 1.032568
ERR551360 151 1573 1559 1466 24 1442 1236 206 1178 58 0.046925566 978804 1012069 1.033985
ERR553098 150 1774 2777 1516 24 1492 1284 208 1209 75 0.058411215 2740220 2834681 1.034472
ERR551090 150 1576 1769 1439 23 1416 1237 179 1183 54 0.043654002 1559170 1614942 1.03577
ERR552912 101 1634 1780 1491 18 1473 1212 261 1175 37 0.030528053 7453348 7722772 1.036148
ERR552331 150 1646 1687 1438 19 1419 1229 190 1179 50 0.040683483 1891906 1960811 1.036421
ERR551804 151 1595 1566 1465 24 1441 1235 206 1177 58 0.046963563 985532 1021450 1.036445
ERR551556 151 1590 1519 1441 24 1417 1228 189 1182 46 0.037459283 1043540 1082667 1.037494
ERR553291 150 1603 1913 1449 19 1430 1247 183 1185 62 0.049719326 1518524 1577282 1.038694
ERR553139 150 1663 2085 1490 23 1467 1257 210 1206 51 0.040572792 1907698 1989008 1.042622
ERR552090 100 1673 1765 1536 22 1514 1288 226 1234 54 0.041925466 6578088 6873152 1.044856
ERR552482 150 1669 2075 1500 25 1475 1259 216 1211 48 0.038125496 2782946 2908465 1.045103
ERR551934 101 1695 1722 1545 19 1526 1263 263 1226 37 0.029295329 9843072 10403752 1.056962
ERR551225 101 1642 1750 1466 18 1448 1195 253 1151 44 0.036820084 4710218 4982704 1.05785
ERR553313 151 1786 2053 1506 24 1482 1294 188 1213 81 0.0625966 2096346 2219112 1.058562
ERR552555 150 1653 1981 1469 21 1448 1242 206 1188 54 0.043478261 1940278 2068603 1.066137
ERR551930 150 1648 2204 1490 19 1471 1274 197 1199 75 0.058869702 1774338 1894144 1.067522
ERR550910 101 1720 1689 1562 19 1543 1284 259 1252 32 0.024922118 12285252 13127870 1.068588
ERR553116 150 1720 2098 1496 20 1476 1284 192 1181 103 0.080218069 1192486 1274638 1.068891
ERR553068 150 1692 1833 1472 24 1448 1261 187 1194 67 0.053132435 1778566 1903448 1.070215
ERR553086 101 1688 1764 1531 19 1512 1254 258 1216 38 0.03030303 8614066 9230646 1.071578
ERR551520 101 1681 1665 1534 19 1515 1280 235 1251 29 0.02265625 15067184 16187939 1.074384
ERR551007 101 1648 1720 1498 19 1479 1254 225 1218 36 0.028708134 6431514 6962325 1.082533
ERR551990 101 1721 1865 1550 19 1531 1281 250 1232 49 0.038251366 4992594 5490661 1.099761
ERR552190 101 1660 1735 1506 19 1487 1269 218 1225 44 0.034672971 5801280 6418256 1.106352

In [ ]: