BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695950.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 88,818,088 number of mapped reads = 87,962,092 (99.04%) number of supplementary alignments = 1,413,272 (1.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 44,094,353 number of mapped paired reads (second in pair) = 43,867,739 number of mapped paired reads (both in pair) = 87,455,786 number of mapped paired reads (singletons) = 506,306 number of mapped bases = 8,709,616,063 bp number of sequenced bases = 8,706,638,969 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,227,648 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 87,762.4905 std insert size = 2,841,349.5 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 53.9005 >>>>>>> ACTG content number of A's = 2,440,530,027 bp (28.03%) number of C's = 1,888,343,667 bp (21.69%) number of T's = 2,429,104,259 bp (27.9%) number of G's = 1,948,513,280 bp (22.38%) number of N's = 147,736 bp (0%) GC percentage = 44.07% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 35,426,196 number of insertions = 1,332,856 mapped reads with insertion percentage = 1.46% number of deletions = 1,128,204 mapped reads with deletion percentage = 1.23% homopolymer indels = 41.29% >>>>>>> Coverage mean coverageData = 2.8135X std coverageData = 10.6583X There is a 70.13% of reference with a coverageData >= 1X There is a 50.56% of reference with a coverageData >= 2X There is a 36.16% of reference with a coverageData >= 3X There is a 26.11% of reference with a coverageData >= 4X There is a 19.16% of reference with a coverageData >= 5X There is a 14.3% of reference with a coverageData >= 6X There is a 10.87% of reference with a coverageData >= 7X There is a 8.39% of reference with a coverageData >= 8X There is a 6.58% of reference with a coverageData >= 9X There is a 5.23% of reference with a coverageData >= 10X There is a 4.21% of reference with a coverageData >= 11X There is a 3.43% of reference with a coverageData >= 12X There is a 2.82% of reference with a coverageData >= 13X There is a 2.34% of reference with a coverageData >= 14X There is a 1.96% of reference with a coverageData >= 15X There is a 1.66% of reference with a coverageData >= 16X There is a 1.41% of reference with a coverageData >= 17X There is a 1.21% of reference with a coverageData >= 18X There is a 1.04% of reference with a coverageData >= 19X There is a 0.9% of reference with a coverageData >= 20X There is a 0.78% of reference with a coverageData >= 21X There is a 0.69% of reference with a coverageData >= 22X There is a 0.6% of reference with a coverageData >= 23X There is a 0.53% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.38% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 768084755 3.0815760936459213 8.93155518206559 chr2 243199373 689853554 2.8365762028506545 22.566005560922274 chr3 198022430 509451211 2.572694472035314 4.597962608683274 chr4 191154276 493561082 2.582003878375182 6.384595379644971 chr5 180915260 443502468 2.451437584645983 5.1619188342865785 chr6 171115067 556050162 3.2495686776664736 7.858034000619809 chr7 159138663 432551360 2.7180783842578844 5.8871587382265265 chr8 146364022 382660581 2.614444286041825 7.235829080247242 chr9 141213431 326661877 2.3132493466574013 14.238116258965427 chr10 135534747 395268358 2.9163617946621465 15.157739799748224 chr11 135006516 462826151 3.4281763926120425 7.190162921521824 chr12 133851895 473739094 3.539278199983646 5.40703618259105 chr13 115169878 239365215 2.0783664891960725 4.830944172770193 chr14 107349540 288508092 2.6875577855294024 10.387418632797846 chr15 102531392 259145662 2.5274762874574064 5.446248572385121 chr16 90354753 314199496 3.4773986488569117 16.355590796762474 chr17 81195210 366394353 4.51251192034604 9.072212631817612 chr18 78077248 230030763 2.9461945559351683 10.986107139159607 chr19 59128983 306991827 5.191901017475643 9.761379535522677 chr20 63025520 241244336 3.8277246423353586 6.027786440219417 chr21 48129895 110414723 2.2940985638967217 6.365467737266795 chr22 51304566 151900735 2.960764447359325 6.317740175004873 chrMT 16571 5790803 349.4540462253334 121.98373688680074 chrX 155270560 197948937 1.2748645783205779 3.505950297906219 chrY 59373566 63470468 1.0690021212470209 19.035034460707706