BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524309.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 = 687,278 number of mapped reads = 632,027 (91.96%) number of supplementary alignments = 2,781 (0.4%) number of secondary alignments = 0 number of mapped bases = 37,005,570 bp number of sequenced bases = 36,996,012 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,402 duplication rate = 1.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3263 >>>>>>> ACTG content number of A's = 8,699,983 bp (23.52%) number of C's = 7,125,218 bp (19.26%) number of T's = 11,664,959 bp (31.53%) number of G's = 9,500,527 bp (25.68%) number of N's = 5,325 bp (0.01%) GC percentage = 44.94% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 186,894 number of insertions = 2,381 mapped reads with insertion percentage = 0.38% number of deletions = 5,855 mapped reads with deletion percentage = 0.92% homopolymer indels = 42.31% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 0.1375X There is a 1.13% of reference with a coverageData >= 1X There is a 0.04% 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 3179642 0.012756806732288944 0.2122408482904949 chr2 243199373 2379604 0.0097845811469259 0.16270459119803277 chr3 198022430 2581177 0.013034770859038545 0.11850653059040822 chr4 191154276 1898266 0.009930544268860614 0.11028235536053922 chr5 180915260 2159089 0.011934255849948755 0.11310677757519942 chr6 171115067 2296324 0.013419765075392222 0.12454796825666657 chr7 159138663 1685226 0.010589670468703134 0.1534345354310202 chr8 146364022 3803994 0.025989952640137204 0.18486851470519983 chr9 141213431 1557787 0.011031436521077092 0.11821570151656081 chr10 135534747 1891126 0.01395307138471288 0.14081156907426606 chr11 135006516 1786466 0.013232442795575882 0.12904470078204056 chr12 133851895 1479255 0.011051431135883433 0.10907889521877769 chr13 115169878 913484 0.007931622537622206 0.0917491673782308 chr14 107349540 785438 0.007316640574333155 0.09036787035383986 chr15 102531392 1141648 0.01113461914181366 0.1092785936888378 chr16 90354753 1199013 0.013270060070885258 0.12142988143200632 chr17 81195210 1137368 0.014007821397345976 0.12631230183996983 chr18 78077248 860436 0.011020316699686956 0.16909197682179816 chr19 59128983 692976 0.011719734804165327 0.15193912435994492 chr20 63025520 871153 0.013822226298172549 0.12418991559611707 chr21 48129895 542168 0.011264682792264558 0.11435934433845071 chr22 51304566 286175 0.005577963567609167 0.07712263538701819 chrMT 16571 16181 0.9764649085752217 1.0939173898508447 chrX 155270560 1754831 0.011301762549191553 0.1145717930870528 chrY 59373566 106743 0.0017978202623032612 0.06021959116653046