BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524325.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 = 1,177,562 number of mapped reads = 1,078,375 (91.58%) number of supplementary alignments = 4,652 (0.4%) number of secondary alignments = 0 number of mapped bases = 62,645,194 bp number of sequenced bases = 62,629,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,088 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5206 >>>>>>> ACTG content number of A's = 15,291,820 bp (24.42%) number of C's = 12,948,202 bp (20.67%) number of T's = 18,945,099 bp (30.25%) number of G's = 15,435,708 bp (24.65%) number of N's = 8,546 bp (0.01%) GC percentage = 45.32% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 314,045 number of insertions = 4,156 mapped reads with insertion percentage = 0.38% number of deletions = 9,848 mapped reads with deletion percentage = 0.91% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.2063X There is a 1.88% 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 5327833 0.021375405118850235 0.36564090606025773 chr2 243199373 4068781 0.016730228165514227 0.2538244574479485 chr3 198022430 4314652 0.02178870343122241 0.1561993565140945 chr4 191154276 3281900 0.01716885475269201 0.14690685147621613 chr5 180915260 3654196 0.02019838459176965 0.15058730885550745 chr6 171115067 4010567 0.023437836716038572 0.17015993389202203 chr7 159138663 2861490 0.017981111227508555 0.24429535938907534 chr8 146364022 6508857 0.044470334383131395 0.2636993830615092 chr9 141213431 2596550 0.01838741528771438 0.16846790566668737 chr10 135534747 3183730 0.023490138657948724 0.2118190918099265 chr11 135006516 2996555 0.022195632394513463 0.1816521421952199 chr12 133851895 2505840 0.018720990091324444 0.1464810864836712 chr13 115169878 1570903 0.013639877260267655 0.12319016199435535 chr14 107349540 1335231 0.012438162287421074 0.12178827106488613 chr15 102531392 1922397 0.018749350442838035 0.14638044478513107 chr16 90354753 1977669 0.02188782476113902 0.16319572256574155 chr17 81195210 1934192 0.023821503756194486 0.17196125531114945 chr18 78077248 1464506 0.018757141645156346 0.2669718608950699 chr19 59128983 1129055 0.019094781319002222 0.2503526315413805 chr20 63025520 1392188 0.022089274313008445 0.15936074078610485 chr21 48129895 901919 0.01873926797471717 0.15183550355524503 chr22 51304566 450841 0.008787541444166977 0.098972557922836 chrMT 16571 71073 4.288998853418623 3.1046927641259225 chrX 155270560 3013650 0.019409023835555175 0.1564150446979042 chrY 59373566 170619 0.0028736525611414345 0.0882714874190618