BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717077.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 = 899,217 number of mapped reads = 821,284 (91.33%) number of supplementary alignments = 1,635 (0.18%) number of secondary alignments = 0 number of mapped bases = 47,610,677 bp number of sequenced bases = 47,595,956 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,488 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4593 >>>>>>> ACTG content number of A's = 11,739,201 bp (24.66%) number of C's = 8,799,778 bp (18.49%) number of T's = 15,388,070 bp (32.33%) number of G's = 11,668,418 bp (24.52%) number of N's = 489 bp (0%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 228,327 number of insertions = 3,707 mapped reads with insertion percentage = 0.45% number of deletions = 9,340 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.35% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.1643X There is a 1.43% of reference with a coverageData >= 1X There is a 0.07% 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 5128432 0.020575403099998696 0.21625092412627894 chr2 243199373 4927173 0.0202598096336375 0.21482362685118858 chr3 198022430 3057874 0.015442058760717157 0.13240725468079614 chr4 191154276 2012138 0.010526251581209725 0.1117174909877311 chr5 180915260 3449752 0.019068330664864866 0.14527888939470562 chr6 171115067 1847537 0.010797044540794295 0.12041079163798141 chr7 159138663 3219033 0.02022784997257392 0.266052443677073 chr8 146364022 2151542 0.014699937666375416 0.14251961995804546 chr9 141213431 1310326 0.009279046551882164 0.12600441046984254 chr10 135534747 2199523 0.01622848050913468 0.19148241604722221 chr11 135006516 2043985 0.015139898877177158 0.15819348172124628 chr12 133851895 1888843 0.014111440110728355 0.12585894972414732 chr13 115169878 1744250 0.01514501908215966 0.1294453114712808 chr14 107349540 1017367 0.009477143544350539 0.10598371312544333 chr15 102531392 1997912 0.019485856585269027 0.14739955255310255 chr16 90354753 1361314 0.015066324181086522 0.14016280736905257 chr17 81195210 1735199 0.02137070647394101 0.16016512951916276 chr18 78077248 1589162 0.020353714311242117 0.2652336247641892 chr19 59128983 720411 0.012183720460742576 0.1701738857909012 chr20 63025520 1201835 0.01906902156459796 0.14607325429987653 chr21 48129895 605103 0.012572290049666637 0.1218332795406928 chr22 51304566 523815 0.010209909971755731 0.10574993561493136 chrMT 16571 23179 1.3987689336793192 1.5352618657513966 chrX 155270560 1753049 0.011290285808204724 0.12096597535139313 chrY 59373566 101923 0.0017166393542877314 0.05170752694271687