BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524301.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 = 1,327,725 number of mapped reads = 1,167,176 (87.91%) number of supplementary alignments = 10,587 (0.8%) number of secondary alignments = 0 number of mapped bases = 66,560,840 bp number of sequenced bases = 66,545,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,461 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4758 >>>>>>> ACTG content number of A's = 16,034,836 bp (24.1%) number of C's = 13,962,310 bp (20.98%) number of T's = 20,866,361 bp (31.36%) number of G's = 15,672,621 bp (23.55%) number of N's = 9,200 bp (0.01%) GC percentage = 44.53% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 347,735 number of insertions = 4,501 mapped reads with insertion percentage = 0.38% number of deletions = 9,607 mapped reads with deletion percentage = 0.82% homopolymer indels = 39.34% >>>>>>> Coverage mean coverageData = 0.0215X std coverageData = 0.2886X There is a 1.99% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 5703701 0.022883397349690054 0.6471273229420792 chr2 243199373 4463676 0.01835397823990278 0.3041678285530039 chr3 198022430 4579235 0.023124829848820663 0.16326258449817704 chr4 191154276 3544528 0.0185427607175264 0.15703743454525054 chr5 180915260 3921039 0.02167334585263841 0.15976255866788747 chr6 171115067 4162182 0.024323877920113254 0.1809145596789123 chr7 159138663 3205091 0.020140240841410112 0.4001438240981579 chr8 146364022 6459177 0.04413090670602096 0.30945240476697267 chr9 141213431 2723873 0.019289050486989444 0.2095442462138606 chr10 135534747 3373205 0.024888119649494753 0.2696579947060785 chr11 135006516 3198222 0.023689389925446266 0.21999481437306254 chr12 133851895 2685084 0.02006011196180674 0.15775237125314068 chr13 115169878 1682384 0.014607847374814445 0.1267836026235494 chr14 107349540 1474599 0.013736425885010778 0.13970383984948062 chr15 102531392 1999350 0.0194998815582256 0.15571674142161004 chr16 90354753 2078208 0.023000538776305438 0.18274697751786942 chr17 81195210 2017114 0.0248427708974458 0.1853017339979373 chr18 78077248 1547928 0.019825596312001162 0.4012073726380257 chr19 59128983 1296382 0.021924645651355105 0.4218389892478601 chr20 63025520 1424025 0.022594418895710816 0.16412046408023775 chr21 48129895 913087 0.018971306710725215 0.15641029698840583 chr22 51304566 501911 0.009782969414457185 0.1042456643899864 chrMT 16571 27660 1.6691810995111942 1.6211150358633883 chrX 155270560 3366277 0.021680072513424308 0.19158244810024477 chrY 59373566 212902 0.003585804497577255 0.10234589369817114