BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068135.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,180,170 number of mapped reads = 1,977,456 (90.7%) number of supplementary alignments = 19,359 (0.89%) number of secondary alignments = 0 number of mapped bases = 132,089,736 bp number of sequenced bases = 132,034,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,360 duplication rate = 4.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7976 >>>>>>> ACTG content number of A's = 36,719,594 bp (27.81%) number of C's = 24,427,261 bp (18.5%) number of T's = 41,864,239 bp (31.71%) number of G's = 29,020,347 bp (21.98%) number of N's = 2,581 bp (0%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 995,605 number of insertions = 10,607 mapped reads with insertion percentage = 0.53% number of deletions = 34,630 mapped reads with deletion percentage = 1.73% homopolymer indels = 47.49% >>>>>>> Coverage mean coverageData = 0.0427X std coverageData = 0.4409X There is a 3.27% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 18602223 0.07463260442588827 0.9096163377235019 chr2 243199373 16130708 0.06632709534164793 0.48734822543111367 chr3 198022430 4862289 0.024554233578489064 0.19266613320045065 chr4 191154276 7435767 0.03889929723570505 0.2602093385658766 chr5 180915260 7594548 0.04197848208050554 0.25743577495124637 chr6 171115067 15648522 0.09145028707495408 0.411619507451093 chr7 159138663 10263310 0.06449287562507673 0.45236827197384033 chr8 146364022 2644959 0.01807110083378277 0.619991808008213 chr9 141213431 7836908 0.055496902415748256 0.44018613834030296 chr10 135534747 2070837 0.01527901180942183 0.2552624205018865 chr11 135006516 8572454 0.06349659449029853 0.4933505280318563 chr12 133851895 8309804 0.06208207959999371 0.3221226497077369 chr13 115169878 2191362 0.01902721473752017 0.17246428805486586 chr14 107349540 550544 0.005128517551169758 0.1857184784753783 chr15 102531392 1381542 0.013474331841705612 0.14870135686724245 chr16 90354753 2673617 0.029590219786224194 0.24751127531355163 chr17 81195210 2161616 0.02662245716218974 0.23807498140144204 chr18 78077248 2800985 0.03587453543444564 0.7168464391955439 chr19 59128983 2613823 0.044205444900007836 0.6850758423903061 chr20 63025520 1001225 0.015886025216452004 0.16666058747047335 chr21 48129895 1155716 0.02401243551435132 0.21182051886678174 chr22 51304566 2961200 0.05771805963625148 0.2955778697397352 chrMT 16571 10332 0.623498883591817 1.2683211806736558 chrX 155270560 2421313 0.015594153843458799 0.20308714812159484 chrY 59373566 194132 0.0032696705466537077 0.10166399006828973