BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716929.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,521,302 number of mapped reads = 2,299,872 (91.22%) number of supplementary alignments = 13,646 (0.54%) number of secondary alignments = 0 number of mapped bases = 133,771,670 bp number of sequenced bases = 133,736,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,011 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5404 >>>>>>> ACTG content number of A's = 33,373,797 bp (24.95%) number of C's = 25,465,376 bp (19.04%) number of T's = 42,505,169 bp (31.78%) number of G's = 32,388,652 bp (24.22%) number of N's = 3,759 bp (0%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 650,424 number of insertions = 7,275 mapped reads with insertion percentage = 0.31% number of deletions = 22,290 mapped reads with deletion percentage = 0.96% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.3864X There is a 3.74% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 13628524 0.05467799416234955 0.8385509957420121 chr2 243199373 12551700 0.0516107416115748 0.457351561955942 chr3 198022430 9098758 0.04594811809955064 0.24435709455375038 chr4 191154276 6163981 0.03224610575805273 0.21591216199752852 chr5 180915260 5786333 0.031983664617346266 0.20434138174355773 chr6 171115067 9130857 0.05336091765665498 0.3012913569202265 chr7 159138663 9571660 0.06014666592995066 0.4844875203880934 chr8 146364022 7631548 0.05214087380025673 0.3044971721864956 chr9 141213431 5489921 0.03887676236688846 0.31274559004445296 chr10 135534747 7006939 0.051698469618274345 0.37829254541474133 chr11 135006516 4346644 0.03219580897858293 0.2805841749241002 chr12 133851895 5362086 0.04005984375492032 0.2333962271755248 chr13 115169878 3027932 0.02629100640360147 0.18221306075403765 chr14 107349540 2920762 0.02720796009000132 0.21857640791539923 chr15 102531392 3898042 0.03801803451571203 0.22260596180193218 chr16 90354753 2697677 0.029856503509007433 0.21822271584641204 chr17 81195210 2902080 0.03574200990427884 0.2244434107437668 chr18 78077248 4547832 0.05824785217839645 0.5436027944917093 chr19 59128983 3273315 0.05535889227115576 0.5733152326969598 chr20 63025520 2042891 0.03241371114431107 0.2050821407276529 chr21 48129895 1671288 0.03472453035686032 0.23656331937014827 chr22 51304566 2042165 0.03980474174559824 0.22516287754145647 chrMT 16571 107726 6.500875022629896 3.8250525853044057 chrX 155270560 8572149 0.05520781917705456 0.3130725166885062 chrY 59373566 298860 0.005033553147203589 0.10815104622555907