BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717060.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 = 1,131,697 number of mapped reads = 1,024,109 (90.49%) number of supplementary alignments = 5,167 (0.46%) number of secondary alignments = 0 number of mapped bases = 59,168,292 bp number of sequenced bases = 59,150,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,727 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4327 >>>>>>> ACTG content number of A's = 14,393,358 bp (24.33%) number of C's = 10,939,640 bp (18.49%) number of T's = 19,093,150 bp (32.28%) number of G's = 14,724,093 bp (24.89%) number of N's = 701 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 296,120 number of insertions = 4,191 mapped reads with insertion percentage = 0.41% number of deletions = 11,099 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.01% >>>>>>> Coverage mean coverageData = 0.0191X std coverageData = 0.2075X There is a 1.77% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4879173 0.019575369483231898 0.271118333818413 chr2 243199373 5399254 0.02220093717100167 0.22993274967767013 chr3 198022430 4519383 0.022822581260112808 0.1649759479668928 chr4 191154276 3331308 0.017427326606076026 0.1477989554118323 chr5 180915260 2961610 0.01637015031236171 0.1350528243459745 chr6 171115067 3308048 0.019332301111742545 0.1563772759072948 chr7 159138663 3726040 0.023413794798565073 0.45795399750257426 chr8 146364022 4413709 0.03015569632269329 0.22649556624546535 chr9 141213431 2462094 0.01743526789601196 0.1525154163788937 chr10 135534747 2861512 0.0211127556832345 0.2561361523825701 chr11 135006516 1766331 0.013083301845964235 0.13954467574225407 chr12 133851895 2780915 0.02077605998779472 0.163328699266606 chr13 115169878 1541145 0.013381493727031646 0.12265673921636278 chr14 107349540 1897464 0.01767556712399513 0.14283709390333205 chr15 102531392 1400160 0.013655915253740044 0.12662023413566764 chr16 90354753 1808200 0.02001222890842278 0.15550844748997875 chr17 81195210 2473642 0.03046536858516654 0.18987805460180326 chr18 78077248 1402488 0.01796282573893998 0.235737597177797 chr19 59128983 1205484 0.020387362319422946 0.26045494418418996 chr20 63025520 1258261 0.019964309695501125 0.1536760709792732 chr21 48129895 621994 0.012923236171614337 0.12669544271228333 chr22 51304566 893375 0.017413167475191196 0.13922749771971127 chrMT 16571 58445 3.5269446623619576 2.4620396004114418 chrX 155270560 2063144 0.013287412629928042 0.13454931765300007 chrY 59373566 135113 0.002275642328776412 0.06796711522432283