notebook.community

Edit and run

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 




In [ ]:

Content source: zhangfang615/Tuberculosis

Similar notebooks:

notebook.community | gallery | about