BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716691.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 = 1,523,714 number of mapped reads = 1,351,843 (88.72%) number of supplementary alignments = 22,646 (1.49%) number of secondary alignments = 0 number of mapped bases = 106,985,475 bp number of sequenced bases = 106,939,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,655 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2917 >>>>>>> ACTG content number of A's = 27,108,900 bp (25.35%) number of C's = 19,942,594 bp (18.65%) number of T's = 32,824,594 bp (30.69%) number of G's = 27,056,713 bp (25.3%) number of N's = 6,410 bp (0.01%) GC percentage = 43.95% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 847,556 number of insertions = 9,235 mapped reads with insertion percentage = 0.67% number of deletions = 26,544 mapped reads with deletion percentage = 1.94% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.466X There is a 3.02% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% 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 9212900 0.03696239537152447 0.7345554252986177 chr2 243199373 8263392 0.03397785075704122 0.8217001442780288 chr3 198022430 7998441 0.04039159099300014 0.23007184398043176 chr4 191154276 4476051 0.023415908310625497 0.18029524951248335 chr5 180915260 6798159 0.03757648193966612 0.218519905808284 chr6 171115067 8666521 0.05064732844361391 0.30999148428718365 chr7 159138663 4739853 0.029784421401102257 0.6385338671470526 chr8 146364022 7734165 0.05284198189087753 0.643014964271497 chr9 141213431 4098469 0.029023223718712705 0.4541894707523199 chr10 135534747 5180713 0.03822424223066576 0.3840072741081723 chr11 135006516 4249818 0.03147861396556593 0.32089036151772077 chr12 133851895 4013554 0.02998503681998675 0.19903825488473498 chr13 115169878 4813669 0.04179624988401915 0.22593026825096943 chr14 107349540 2551679 0.0237698177374584 0.22273587900700928 chr15 102531392 2107828 0.02055787948338788 0.1599194528531561 chr16 90354753 2723702 0.03014453484256661 0.2351934344072053 chr17 81195210 3122564 0.0384574902879123 0.2517082212354883 chr18 78077248 3350369 0.04291095147206008 0.9428753761608096 chr19 59128983 2138334 0.03616388937384565 0.6160744369521527 chr20 63025520 2023140 0.03210033015197653 0.25282621023193896 chr21 48129895 2339490 0.04860783510955093 0.2523472305012736 chr22 51304566 1608570 0.031353349719399244 0.19648665166789928 chrMT 16571 2036 0.12286524651499607 0.528905213374239 chrX 155270560 4509482 0.029042736755763618 0.2767494142700126 chrY 59373566 262576 0.004422439440474234 0.1284993931421354