BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716335.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 = 985,562 number of mapped reads = 866,926 (87.96%) number of supplementary alignments = 3,229 (0.33%) number of secondary alignments = 0 number of mapped bases = 48,891,601 bp number of sequenced bases = 48,876,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,728 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4073 >>>>>>> ACTG content number of A's = 12,191,633 bp (24.94%) number of C's = 9,374,788 bp (19.18%) number of T's = 16,095,610 bp (32.93%) number of G's = 11,214,056 bp (22.94%) number of N's = 788 bp (0%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 272,155 number of insertions = 3,040 mapped reads with insertion percentage = 0.35% number of deletions = 8,725 mapped reads with deletion percentage = 1% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 0.0158X std coverageData = 0.1719X There is a 1.47% of reference with a coverageData >= 1X There is a 0.08% 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 3890742 0.015609758500862471 0.2832172294521578 chr2 243199373 4113945 0.016915935881134037 0.18157190148735083 chr3 198022430 3273570 0.016531309104731218 0.13507044838681223 chr4 191154276 3221299 0.01685182810140224 0.14663778797795682 chr5 180915260 2968406 0.016407714860537468 0.135633175317233 chr6 171115067 2843641 0.01661829697322913 0.1446381394948216 chr7 159138663 2661744 0.01672594170280292 0.1936002811866972 chr8 146364022 2491079 0.017019749566597724 0.18354648083473818 chr9 141213431 2064871 0.014622341411703254 0.1697939894281122 chr10 135534747 2309136 0.017037225147880343 0.17903050315794153 chr11 135006516 2229004 0.01651034384147799 0.15975139692914084 chr12 133851895 2229325 0.016655162035621535 0.1392654331991807 chr13 115169878 1560758 0.013551789991476765 0.1216350588545361 chr14 107349540 1501265 0.01398482937141603 0.13241833799356284 chr15 102531392 1362567 0.013289266569208385 0.12116377555286396 chr16 90354753 1412927 0.01563755035664809 0.14089605853929094 chr17 81195210 1280875 0.01577525324461874 0.13572545179868248 chr18 78077248 1315837 0.016853014593957 0.2640860741151575 chr19 59128983 969212 0.01639148774129939 0.2206119169051313 chr20 63025520 1018754 0.016164150648816544 0.13765647588121843 chr21 48129895 651603 0.013538425546118478 0.13092322942862297 chr22 51304566 556413 0.010845292015529378 0.10914453921795991 chrMT 16571 3295 0.1988413493452417 0.46335887988300933 chrX 155270560 2808180 0.01808572082177072 0.15612949831888362 chrY 59373566 153153 0.002579481245913375 0.07689094989689127