BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053671.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 = 10,711,010 number of mapped reads = 6,588,710 (61.51%) number of supplementary alignments = 118 (0%) number of secondary alignments = 0 number of mapped bases = 303,229,117 bp number of sequenced bases = 303,173,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,521,451 duplication rate = 17.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1912 >>>>>>> ACTG content number of A's = 89,153,158 bp (29.41%) number of C's = 61,922,513 bp (20.42%) number of T's = 90,031,205 bp (29.7%) number of G's = 61,859,855 bp (20.4%) number of N's = 206,707 bp (0.07%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 4,691,823 number of insertions = 16,728 mapped reads with insertion percentage = 0.25% number of deletions = 39,362 mapped reads with deletion percentage = 0.6% homopolymer indels = 37.4% >>>>>>> Coverage mean coverageData = 0.098X std coverageData = 0.7873X There is a 4.27% of reference with a coverageData >= 1X There is a 1.85% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 28539761 0.11450226637549682 0.9110091138213489 chr2 243199373 29662005 0.12196579552859291 0.9209972884059817 chr3 198022430 25536452 0.1289573711422489 0.845659515893961 chr4 191154276 20337419 0.10639269717408781 0.7651325770112082 chr5 180915260 13666991 0.07554360533213174 0.6524088403938775 chr6 171115067 22627287 0.13223433445518856 0.9561500769194886 chr7 159138663 14567917 0.09154228598740961 0.8630670858355627 chr8 146364022 13640193 0.09319361967246295 0.7605606844804377 chr9 141213431 12057307 0.08538357091543226 0.7268574071597723 chr10 135534747 14314650 0.10561608972494707 0.7974378354112609 chr11 135006516 11695099 0.08662618180592113 0.8492845165471683 chr12 133851895 9107494 0.06804157684879994 0.6155417492025497 chr13 115169878 6071283 0.05271589329980882 0.5002591515688214 chr14 107349540 11314534 0.10539899844936457 0.829971182649594 chr15 102531392 8725901 0.08510467701443086 0.6562389923463082 chr16 90354753 8778978 0.0971612196206214 0.7398275142459063 chr17 81195210 9486366 0.11683405954612347 0.7929235858898713 chr18 78077248 7043924 0.09021737036633258 0.7713591588667201 chr19 59128983 4812118 0.0813834054950683 0.7530086902523973 chr20 63025520 6504454 0.10320349598067577 0.7320529123645684 chr21 48129895 3870926 0.08042664543523313 0.678454733627394 chr22 51304566 3541199 0.06902307681542419 0.5759804904104642 chrMT 16571 57275 3.4563393880876228 6.360514267739315 chrX 155270560 16497989 0.10625316866249468 0.8043880584953432 chrY 59373566 771595 0.012995598074739186 0.23555276307820183