BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013332.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 = 1,818,379 number of mapped reads = 1,314,242 (72.28%) number of supplementary alignments = 5,355 (0.29%) number of secondary alignments = 0 number of mapped bases = 77,542,738 bp number of sequenced bases = 77,510,657 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,928 duplication rate = 5.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6138 >>>>>>> ACTG content number of A's = 20,754,921 bp (26.78%) number of C's = 12,519,147 bp (16.15%) number of T's = 25,213,162 bp (32.53%) number of G's = 19,009,126 bp (24.52%) number of N's = 14,301 bp (0.02%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 728,758 number of insertions = 4,627 mapped reads with insertion percentage = 0.35% number of deletions = 19,850 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.025X std coverageData = 0.2082X There is a 2.16% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.05% 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 5552438 0.02227652624384033 0.23079473483088714 chr2 243199373 9358727 0.038481706940913865 0.2758367721148748 chr3 198022430 4913357 0.02481212355590223 0.18058903773375623 chr4 191154276 4323369 0.022617171273741216 0.17798414676460758 chr5 180915260 2967729 0.016403972777089118 0.14989887151641754 chr6 171115067 4001765 0.023386397645509496 0.19794672874510677 chr7 159138663 4557829 0.028640613877722473 0.29590949068922406 chr8 146364022 4713795 0.032205967939306836 0.2500522931473137 chr9 141213431 2760917 0.01955137680919317 0.18144216022599985 chr10 135534747 4169781 0.030765402173953224 0.21402969315527637 chr11 135006516 3252919 0.0240945333334874 0.19195330809880493 chr12 133851895 4428756 0.03308698767395112 0.20812662291051517 chr13 115169878 1492080 0.012955470874076988 0.12912262295655375 chr14 107349540 2667181 0.02484576086679086 0.1827221894686061 chr15 102531392 2127434 0.02074909896863587 0.17226946392974618 chr16 90354753 2854819 0.03159567045687126 0.20845650653462214 chr17 81195210 2334669 0.02875377747037048 0.20399881422795285 chr18 78077248 1706668 0.021858711003748494 0.24215203877551458 chr19 59128983 1347815 0.022794489802065426 0.20288512563656358 chr20 63025520 1640003 0.026021252978158688 0.18936947014155794 chr21 48129895 1349515 0.028039018161165736 0.19589789697989354 chr22 51304566 698653 0.013617754801785089 0.1323292753516717 chrMT 16571 21141 1.2757829943877859 1.729178478414342 chrX 155270560 4160209 0.02679328908197407 0.1982799405753303 chrY 59373566 141169 0.0023776405816689533 0.05686836540094847