BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524859.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 = 1,896,970 number of mapped reads = 1,744,191 (91.95%) number of supplementary alignments = 10,371 (0.55%) number of secondary alignments = 0 number of mapped bases = 102,027,287 bp number of sequenced bases = 101,996,907 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,345 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6082 >>>>>>> ACTG content number of A's = 26,751,357 bp (26.23%) number of C's = 17,990,558 bp (17.64%) number of T's = 32,051,929 bp (31.42%) number of G's = 25,188,522 bp (24.7%) number of N's = 14,541 bp (0.01%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 491,945 number of insertions = 6,970 mapped reads with insertion percentage = 0.4% number of deletions = 19,331 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3257X There is a 2.98% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8640383 0.03466544221769462 0.6598314673527615 chr2 243199373 6569136 0.027011319638558445 0.3122749771065702 chr3 198022430 7501749 0.03788332968139013 0.20868527080470634 chr4 191154276 5598769 0.029289268946303876 0.20076669377708328 chr5 180915260 5324106 0.029428728123874127 0.18533640756709469 chr6 171115067 6571043 0.0384013115572108 0.237048449573853 chr7 159138663 4741462 0.029794532080491338 0.4492210733887314 chr8 146364022 11226348 0.07670155442981746 0.42886618542637445 chr9 141213431 4268045 0.030224072666289088 0.28028590834643546 chr10 135534747 5083204 0.037504803104107316 0.31069465032266214 chr11 135006516 4990917 0.036967971234810625 0.29660006039867387 chr12 133851895 4217444 0.03150828757411316 0.19614874681589786 chr13 115169878 2723613 0.02364865750747778 0.1633663894932611 chr14 107349540 2196974 0.02046561168310549 0.16915989177662727 chr15 102531392 3095894 0.030194596402241373 0.1886372099931994 chr16 90354753 3037305 0.033615331780055886 0.21887906700512477 chr17 81195210 2659416 0.03275336069701649 0.2249194637161761 chr18 78077248 2487097 0.03185431177082471 0.4885854666803464 chr19 59128983 1585904 0.02682109381113489 0.4583878016517855 chr20 63025520 2215729 0.03515606059259804 0.2040244136608462 chr21 48129895 1274892 0.02648856807188131 0.1913425473749772 chr22 51304566 637049 0.012417003975825465 0.11829169915045538 chrMT 16571 18840 1.1369259549815944 1.257974115451803 chrX 155270560 5103442 0.032868059469869884 0.2306472224657617 chrY 59373566 258526 0.004354227266726745 0.10737771008188517