BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524372.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 = 537,245 number of mapped reads = 490,279 (91.26%) number of supplementary alignments = 2,502 (0.47%) number of secondary alignments = 0 number of mapped bases = 28,730,633 bp number of sequenced bases = 28,722,472 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,401 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0454 >>>>>>> ACTG content number of A's = 7,299,598 bp (25.41%) number of C's = 5,479,681 bp (19.08%) number of T's = 9,157,418 bp (31.88%) number of G's = 6,781,566 bp (23.61%) number of N's = 4,209 bp (0.01%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 148,956 number of insertions = 2,490 mapped reads with insertion percentage = 0.51% number of deletions = 5,258 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.25% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1245X There is a 0.87% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2354387 0.009445862122847029 0.18862402185344015 chr2 243199373 2360522 0.009706118773587463 0.16054020820213996 chr3 198022430 1878618 0.009486894994673077 0.10156889144517166 chr4 191154276 1841842 0.009635369077487965 0.11130886448350573 chr5 180915260 1714600 0.009477365259293219 0.10146671122418359 chr6 171115067 1531464 0.008949907374316722 0.1016143356215154 chr7 159138663 1582360 0.009943278208891324 0.14964711948950057 chr8 146364022 1492468 0.010196959468632256 0.12179332131082694 chr9 141213431 1252110 0.008866791148215923 0.10990732510055266 chr10 135534747 1407552 0.010385174511743473 0.1273440840655982 chr11 135006516 1302264 0.009645934422898522 0.11574483064176418 chr12 133851895 1300029 0.009712443742391543 0.10403608161422837 chr13 115169878 860164 0.0074686542604482055 0.09024244658791873 chr14 107349540 863501 0.008043825804935912 0.09542355682429188 chr15 102531392 842067 0.008212772533118442 0.0945874395152989 chr16 90354753 865158 0.009575124398823822 0.10501669744948126 chr17 81195210 832359 0.010251331328535267 0.10833752728021175 chr18 78077248 767569 0.009830892092918028 0.16910913743244152 chr19 59128983 592337 0.010017709927464844 0.14139864050234383 chr20 63025520 633522 0.010051832971786667 0.1063454751326557 chr21 48129895 374736 0.007785930137599511 0.09644770584716797 chr22 51304566 374398 0.0072975571024224235 0.08935322451169489 chrMT 16571 16566 0.9996982680586567 1.20127561018542 chrX 155270560 1590755 0.010245052249441233 0.10962501063519743 chrY 59373566 99285 0.0016722088075356632 0.061315759354214495