BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054567.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 14,459,313 number of mapped reads = 10,779,631 (74.55%) number of supplementary alignments = 306 (0%) number of secondary alignments = 0 number of mapped bases = 508,621,075 bp number of sequenced bases = 508,501,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,175,370 duplication rate = 25.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8629 >>>>>>> ACTG content number of A's = 158,846,405 bp (31.24%) number of C's = 94,443,481 bp (18.57%) number of T's = 157,819,809 bp (31.04%) number of G's = 97,310,552 bp (19.14%) number of N's = 80,759 bp (0.02%) GC percentage = 37.71% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 2,772,038 number of insertions = 24,409 mapped reads with insertion percentage = 0.23% number of deletions = 80,968 mapped reads with deletion percentage = 0.75% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 0.1643X std coverageData = 1.5951X There is a 4.64% of reference with a coverageData >= 1X There is a 2.3% of reference with a coverageData >= 2X There is a 1.53% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 41789469 0.167660440854027 1.6597658838209441 chr2 243199373 53781353 0.2211410018725665 1.9655253332029123 chr3 198022430 33798735 0.17068134655250922 1.5614939289291379 chr4 191154276 25486533 0.13332965149050602 1.403552055281506 chr5 180915260 26607217 0.147070053681486 1.424618338998408 chr6 171115067 32148005 0.18787360788047963 1.7595645425331459 chr7 159138663 26699535 0.1677752878946834 1.6843019799360188 chr8 146364022 27857285 0.19032877492256942 1.7559677675184229 chr9 141213431 29044561 0.2056784598626458 1.7734878471263456 chr10 135534747 22697340 0.16746510029638378 1.5577181777399776 chr11 135006516 24129161 0.1787258994225138 1.6432560189031973 chr12 133851895 27161628 0.20292299933445096 1.778225200883538 chr13 115169878 8327466 0.07230593749521902 0.9917205252917947 chr14 107349540 9773770 0.09104622153015281 1.272031557927374 chr15 102531392 14782408 0.1441744592719467 1.3964395604092026 chr16 90354753 10910977 0.12075708955786753 1.2438794987484314 chr17 81195210 12040161 0.1482865922755788 1.4244659871169871 chr18 78077248 16424835 0.21036646937146145 1.9103723371006487 chr19 59128983 8586552 0.14521731246417682 1.4331302609813963 chr20 63025520 10063616 0.15967525535687765 1.473020999582527 chr21 48129895 4780889 0.09933304446228275 1.1337324483847735 chr22 51304566 6052100 0.11796415936936296 1.22464757657646 chrMT 16571 40337 2.4341922635930238 6.481544205881995 chrX 155270560 34482068 0.22207730815165477 1.8652314112816615 chrY 59373566 1155074 0.019454347747952346 0.4121185851549507