BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524331.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 = 3,331,797 number of mapped reads = 3,039,249 (91.22%) number of supplementary alignments = 14,938 (0.45%) number of secondary alignments = 0 number of mapped bases = 176,696,527 bp number of sequenced bases = 176,648,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,112 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.989 >>>>>>> ACTG content number of A's = 43,320,631 bp (24.52%) number of C's = 31,790,998 bp (18%) number of T's = 58,034,513 bp (32.85%) number of G's = 43,478,386 bp (24.61%) number of N's = 23,785 bp (0.01%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 908,352 number of insertions = 12,238 mapped reads with insertion percentage = 0.4% number of deletions = 30,580 mapped reads with deletion percentage = 1% homopolymer indels = 42.42% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.498X There is a 4.88% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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% 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 14388540 0.057727198200240394 1.015867730346896 chr2 243199373 11624403 0.0477978329327354 0.685334820854296 chr3 198022430 12487197 0.06305950795574017 0.290368374975508 chr4 191154276 9187548 0.048063523308262274 0.2962870979968208 chr5 180915260 10367477 0.05730570765561733 0.27367106053575374 chr6 171115067 11200661 0.06545689515465053 0.33141480709519633 chr7 159138663 8044645 0.05055116618643453 0.6319317378663514 chr8 146364022 18615782 0.1271882375574511 0.590037858010452 chr9 141213431 7299229 0.051689339663448866 0.36586548686917286 chr10 135534747 8934152 0.06591779744864983 0.4880684099536103 chr11 135006516 8444681 0.06255017350421813 0.39273788424888534 chr12 133851895 7053002 0.05269258235006684 0.2687731858705284 chr13 115169878 4495841 0.03903660469276524 0.22515560391689077 chr14 107349540 3759008 0.03501652638660585 0.22818424188153028 chr15 102531392 5417497 0.05283744709132594 0.2678802933111148 chr16 90354753 5955511 0.06591253699736194 0.32977002687774365 chr17 81195210 5361429 0.06603134593777145 0.3386711944531608 chr18 78077248 4144608 0.05308342835034349 0.6943556812387809 chr19 59128983 3100505 0.05243629845620717 0.686344141272372 chr20 63025520 3978660 0.06312776157975372 0.294366056867504 chr21 48129895 2564759 0.05328827332783502 0.3001199541932078 chr22 51304566 1281302 0.024974424303676985 0.17769688719186427 chrMT 16571 6780 0.40914851246152917 0.743323554581487 chrX 155270560 8483302 0.05463561154155688 0.31217619712030437 chrY 59373566 500008 0.008421390758304798 0.22910238491375587