BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716619.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 = 804,322 number of mapped reads = 745,494 (92.69%) number of supplementary alignments = 12,585 (1.56%) number of secondary alignments = 0 number of mapped bases = 58,635,648 bp number of sequenced bases = 58,609,971 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,550 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6971 >>>>>>> ACTG content number of A's = 14,584,445 bp (24.88%) number of C's = 10,804,041 bp (18.43%) number of T's = 18,117,294 bp (30.91%) number of G's = 15,101,266 bp (25.77%) number of N's = 2,925 bp (0%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 483,247 number of insertions = 5,378 mapped reads with insertion percentage = 0.71% number of deletions = 14,767 mapped reads with deletion percentage = 1.95% homopolymer indels = 43.5% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.2697X There is a 1.73% of reference with a coverageData >= 1X There is a 0.1% 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 5005375 0.02008169520267715 0.4063666480346441 chr2 243199373 4732798 0.01946056826388282 0.44464551873391145 chr3 198022430 4553761 0.022996187856092868 0.16357105829169952 chr4 191154276 2426902 0.01269603825132324 0.12668757180064213 chr5 180915260 3774436 0.02086300514395524 0.15533495987512197 chr6 171115067 4418175 0.025819906320698225 0.20237015169871944 chr7 159138663 3039434 0.019099280732300737 0.40058081906152515 chr8 146364022 4274522 0.029204731747532874 0.3590586314581121 chr9 141213431 2617175 0.018533470799955282 0.25258056590991956 chr10 135534747 2819528 0.020802990099653192 0.21846183290659607 chr11 135006516 2357539 0.01746240899957747 0.2073311486430381 chr12 133851895 2231838 0.016673936517671267 0.13865998740909902 chr13 115169878 1945614 0.0168934276373897 0.1361970967872461 chr14 107349540 1423154 0.013257197003359306 0.14037681746430306 chr15 102531392 1397401 0.013629006421760079 0.12696511544244898 chr16 90354753 1447002 0.01601467495572701 0.14668009907778803 chr17 81195210 1722466 0.021213886878302304 0.17780073058171478 chr18 78077248 1763156 0.022582199618511146 0.5442443271896985 chr19 59128983 1094013 0.01850214470964265 0.3104298607911723 chr20 63025520 1062198 0.016853458725925623 0.15058581759698644 chr21 48129895 1052551 0.02186896522421252 0.15882600098585156 chr22 51304566 846362 0.016496816287267686 0.1368712653677123 chrMT 16571 25947 1.565807736406976 1.6261133247919046 chrX 155270560 2481644 0.0159827078616835 0.1750553952902052 chrY 59373566 122657 0.0020658519988508016 0.06494747937354454