BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524320.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 = 3,210,377 number of mapped reads = 2,913,258 (90.75%) number of supplementary alignments = 12,372 (0.39%) number of secondary alignments = 0 number of mapped bases = 168,116,267 bp number of sequenced bases = 168,071,566 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,443 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8744 >>>>>>> ACTG content number of A's = 41,970,427 bp (24.97%) number of C's = 31,488,252 bp (18.74%) number of T's = 54,076,625 bp (32.17%) number of G's = 40,513,151 bp (24.1%) number of N's = 23,111 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 866,935 number of insertions = 11,733 mapped reads with insertion percentage = 0.4% number of deletions = 27,871 mapped reads with deletion percentage = 0.95% homopolymer indels = 41.28% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.4678X There is a 4.64% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14307157 0.05740068747912969 0.8926616344340599 chr2 243199373 10911507 0.04486650958594371 0.7232892764673925 chr3 198022430 11656141 0.05886273085326748 0.28178336193123854 chr4 191154276 8782892 0.045946615392480156 0.29955503767066377 chr5 180915260 9730297 0.05378372725440629 0.26572940443582405 chr6 171115067 10587019 0.06187075858141703 0.3239090965669388 chr7 159138663 7743301 0.04865757229592912 0.5767417933018477 chr8 146364022 17402391 0.11889801033207464 0.554220421335524 chr9 141213431 6907136 0.04891274116836663 0.3444140196896931 chr10 135534747 8544358 0.06304182646240525 0.4625156445888662 chr11 135006516 8097012 0.05997497187469085 0.3689457202146706 chr12 133851895 6706254 0.05010204749062387 0.26400043896836556 chr13 115169878 4237438 0.03679293643082612 0.2196681092314188 chr14 107349540 3554619 0.03311256853080134 0.22764054360991975 chr15 102531392 5153375 0.05026143602926994 0.2640870866933753 chr16 90354753 5316354 0.058838675592417365 0.3028618270725834 chr17 81195210 5273534 0.06494883134115917 0.32946998565067437 chr18 78077248 3983893 0.051025018197362694 0.6298161142767449 chr19 59128983 3067122 0.051871719153363416 0.58827330450212 chr20 63025520 3846530 0.06103130922204212 0.2976270707709327 chr21 48129895 2419845 0.05027737957874207 0.28879117975619817 chr22 51304566 1214897 0.02368009506210422 0.1747724028289542 chrMT 16571 9429 0.5690060949852151 0.8665036227892786 chrX 155270560 8161323 0.052561947351771 0.30681186783322056 chrY 59373566 502443 0.008462402275113474 0.22730661116156733