BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231776.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,137,240 number of mapped reads = 4,486,393 (87.33%) number of supplementary alignments = 21,282 (0.41%) number of secondary alignments = 0 number of mapped bases = 282,479,267 bp number of sequenced bases = 282,373,952 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 405,555 duplication rate = 6.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4088 >>>>>>> ACTG content number of A's = 71,097,327 bp (25.18%) number of C's = 51,332,000 bp (18.18%) number of T's = 90,749,435 bp (32.14%) number of G's = 69,090,583 bp (24.47%) number of N's = 104,607 bp (0.04%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,779,527 number of insertions = 18,374 mapped reads with insertion percentage = 0.41% number of deletions = 59,030 mapped reads with deletion percentage = 1.3% homopolymer indels = 43.87% >>>>>>> Coverage mean coverageData = 0.0912X std coverageData = 1.1106X There is a 7.18% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% 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 24253985 0.09730762115132303 2.403389788198035 chr2 243199373 21963822 0.09031200092773266 1.2099726694006558 chr3 198022430 31376734 0.15845040382546563 0.491113896924307 chr4 191154276 12851330 0.06723014660681721 0.3719536324404747 chr5 180915260 10288785 0.05687074158365635 0.32435342672570966 chr6 171115067 24645671 0.1440298124068759 0.7734316328206714 chr7 159138663 21431877 0.13467423061107406 2.3653129687266667 chr8 146364022 21204548 0.14487541207360372 0.8728378460920942 chr9 141213431 12639707 0.08950782450714621 0.8068352386957427 chr10 135534747 12044348 0.08886538888806131 0.9167159123271207 chr11 135006516 9676901 0.07167728852435537 0.7540153682250277 chr12 133851895 9889008 0.07388022410889289 0.3733299915807519 chr13 115169878 7464601 0.06481383092200549 0.33007290923548194 chr14 107349540 10091750 0.09400832085540375 0.4617759856217346 chr15 102531392 4174311 0.04071251661149787 0.3310006058037067 chr16 90354753 7451341 0.08246761517902661 0.48016637400015916 chr17 81195210 5361230 0.06602889505427721 0.39890080734761163 chr18 78077248 6265517 0.08024766702842805 1.7626566286941454 chr19 59128983 6178889 0.10449848258002341 1.3629263638013391 chr20 63025520 5203360 0.08255957269372788 0.3886125338674904 chr21 48129895 3730181 0.07750237144710163 0.39252213128548163 chr22 51304566 3413997 0.06654372634201798 0.3109273813735594 chrMT 16571 472778 28.53044475288154 16.483252984467168 chrX 155270560 9714858 0.06256728899541548 0.5336167081499885 chrY 59373566 689738 0.011616920566974198 0.24289598853721162