BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716603.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 = 1,636,334 number of mapped reads = 1,463,771 (89.45%) number of supplementary alignments = 40,474 (2.47%) number of secondary alignments = 0 number of mapped bases = 111,176,901 bp number of sequenced bases = 111,135,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,435 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7555 >>>>>>> ACTG content number of A's = 29,297,530 bp (26.36%) number of C's = 22,686,106 bp (20.41%) number of T's = 33,642,733 bp (30.27%) number of G's = 25,494,614 bp (22.94%) number of N's = 14,041 bp (0.01%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 821,011 number of insertions = 10,021 mapped reads with insertion percentage = 0.68% number of deletions = 24,323 mapped reads with deletion percentage = 1.64% homopolymer indels = 40.71% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.3243X There is a 3.18% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 9393851 0.03768837550860104 0.48084188300168 chr2 243199373 8793274 0.036156647492672604 0.475633958216539 chr3 198022430 8905221 0.04497076922043629 0.2384802098370073 chr4 191154276 4842220 0.025331476236503336 0.18259585552421664 chr5 180915260 7393674 0.0408681611490374 0.22467503860023597 chr6 171115067 8061807 0.04711336728752238 0.2695604937185905 chr7 159138663 6412128 0.04029271001227401 0.4387955226016701 chr8 146364022 8364521 0.057148750667701656 0.41916966626623053 chr9 141213431 5044177 0.03572023542151596 0.30325046536805117 chr10 135534747 5279754 0.03895498473170131 0.34780659911151907 chr11 135006516 4636539 0.03434307570754585 0.256322441977041 chr12 133851895 4300404 0.03212807708101555 0.19827418840821792 chr13 115169878 4199060 0.03645970693830204 0.20909305922690727 chr14 107349540 2718202 0.025321040034265635 0.19200820767710533 chr15 102531392 2534191 0.024716244952570233 0.17115992068992267 chr16 90354753 2924052 0.03236190574280027 0.22371022887614309 chr17 81195210 3211303 0.03955039958637954 0.24361313874294302 chr18 78077248 2857777 0.03660191762906397 0.5924748630353981 chr19 59128983 1659174 0.028060249235133977 0.3763075889732734 chr20 63025520 2101576 0.033344841898964105 0.21757814535437828 chr21 48129895 2355058 0.048931293118341525 0.2515701011365326 chr22 51304566 1247429 0.024314190670670522 0.17135414908033 chrMT 16571 125784 7.590610101985396 5.409636419635756 chrX 155270560 3575981 0.023030644057701603 0.20458431345208342 chrY 59373566 239744 0.004037891205658761 0.12409291333488907