BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524843.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 = 2,167,431 number of mapped reads = 1,985,848 (91.62%) number of supplementary alignments = 8,947 (0.41%) number of secondary alignments = 0 number of mapped bases = 114,414,474 bp number of sequenced bases = 114,381,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,111 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4464 >>>>>>> ACTG content number of A's = 29,650,333 bp (25.92%) number of C's = 21,603,978 bp (18.89%) number of T's = 36,468,432 bp (31.88%) number of G's = 26,643,525 bp (23.29%) number of N's = 15,178 bp (0.01%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 559,766 number of insertions = 7,365 mapped reads with insertion percentage = 0.37% number of deletions = 21,175 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.3611X There is a 3.26% of reference with a coverageData >= 1X There is a 0.29% 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 0.01% 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 9789785 0.03927687305541357 0.704204171742467 chr2 243199373 7527862 0.03095345973609891 0.39248380832400337 chr3 198022430 8277194 0.04179927496092235 0.22521870218437248 chr4 191154276 6296657 0.03294018387535312 0.22516189677498075 chr5 180915260 6962318 0.038483862555320096 0.21931959325964248 chr6 171115067 6987421 0.040834633223735935 0.2605014480391387 chr7 159138663 5220734 0.032806194934539575 0.47451560777539026 chr8 146364022 11661684 0.07967589193469964 0.4591516997686314 chr9 141213431 4851862 0.03435836071428645 0.2983234963006019 chr10 135534747 5749519 0.042420996292559576 0.3245093800073537 chr11 135006516 5637995 0.04176091026599042 0.3142558329480308 chr12 133851895 4224000 0.031557267082397304 0.20393453643214135 chr13 115169878 2938663 0.025515899218022962 0.1769851720341906 chr14 107349540 2508386 0.02336652770007212 0.18405305569002497 chr15 102531392 3447612 0.03362494093516257 0.2092139796854535 chr16 90354753 3310370 0.03663747495386325 0.23224992168743744 chr17 81195210 3182431 0.039194812107758575 0.254206857864766 chr18 78077248 2744027 0.03514502714030085 0.5351138536212825 chr19 59128983 1775698 0.03003092409013698 0.48891548479603125 chr20 63025520 2559778 0.040614944549446 0.22541185223869653 chr21 48129895 1728458 0.035912357589809825 0.22556665395812808 chr22 51304566 721370 0.014060541901865032 0.12923866654340244 chrMT 16571 424529 25.61879186530686 13.94744993894826 chrX 155270560 5588626 0.035992824396331155 0.25242601901304174 chrY 59373566 297495 0.005010563118273879 0.12536875687893895