BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716216.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 = 4,140,310 number of mapped reads = 3,693,552 (89.21%) number of supplementary alignments = 20,995 (0.51%) number of secondary alignments = 0 number of mapped bases = 215,119,707 bp number of sequenced bases = 215,057,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,888 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1481 >>>>>>> ACTG content number of A's = 55,498,464 bp (25.81%) number of C's = 41,485,972 bp (19.29%) number of T's = 67,511,177 bp (31.39%) number of G's = 50,558,928 bp (23.51%) number of N's = 2,769 bp (0%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,092,275 number of insertions = 14,215 mapped reads with insertion percentage = 0.38% number of deletions = 39,822 mapped reads with deletion percentage = 1.07% homopolymer indels = 40.35% >>>>>>> Coverage mean coverageData = 0.0695X std coverageData = 0.6128X There is a 5.71% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 15593478 0.06256144092014118 0.8187734078452085 chr2 243199373 20920575 0.08602232292761709 0.753199705539796 chr3 198022430 16089174 0.0812492504005733 0.37555457561052946 chr4 191154276 11818163 0.061825260974020795 0.33472752488768903 chr5 180915260 10699330 0.05914000842162236 0.289841917116281 chr6 171115067 11622355 0.06792128363541476 0.35698698303062765 chr7 159138663 13451751 0.08452849072886832 1.5282752621437818 chr8 146364022 16917620 0.11558591905871513 0.6296592920309508 chr9 141213431 8841675 0.06261213920933625 0.396888647425922 chr10 135534747 10117418 0.07464814908312774 0.8123679679204346 chr11 135006516 7181190 0.05319143262685188 0.4523058222107527 chr12 133851895 9890569 0.07389188625233882 0.37929035042743364 chr13 115169878 5438628 0.04722266007783737 0.25443464944015287 chr14 107349540 6876403 0.0640561943721417 0.3104786261578711 chr15 102531392 5063914 0.04938891300724758 0.2821767859552838 chr16 90354753 6240593 0.06906767815523772 0.3402106526086445 chr17 81195210 8914908 0.10979598427050069 0.4296151425278966 chr18 78077248 4959653 0.06352238490782872 0.8234715922925888 chr19 59128983 3712913 0.06279345274719168 0.7494521276077623 chr20 63025520 4735403 0.07513469147101047 0.35000825591229345 chr21 48129895 2188306 0.04546666889674287 0.27367672112240843 chr22 51304566 5698970 0.11108114626678647 0.4257644824900394 chrMT 16571 202691 12.231669784563394 7.514152398705938 chrX 155270560 7488166 0.04822656658158507 0.3390029960858866 chrY 59373566 455861 0.0076778443794330966 0.1870612422111087