BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237244.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 = 2,656,557 number of mapped reads = 2,258,508 (85.02%) number of supplementary alignments = 19,126 (0.72%) number of secondary alignments = 0 number of mapped bases = 150,086,751 bp number of sequenced bases = 150,025,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,662 duplication rate = 5.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1117 >>>>>>> ACTG content number of A's = 40,326,826 bp (26.88%) number of C's = 27,983,370 bp (18.65%) number of T's = 47,268,684 bp (31.51%) number of G's = 34,444,175 bp (22.96%) number of N's = 2,509 bp (0%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,210,664 number of insertions = 12,093 mapped reads with insertion percentage = 0.53% number of deletions = 36,539 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.0485X std coverageData = 0.4298X There is a 3.61% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15428292 0.06189871037472761 0.4789461468582434 chr2 243199373 8123700 0.033403457828816034 0.679665457743632 chr3 198022430 5987150 0.030234706240096134 0.2201501391821262 chr4 191154276 7193180 0.03763023328863436 0.3263172914857202 chr5 180915260 10552264 0.058327108503727104 0.31230369143601844 chr6 171115067 13781120 0.08053715106221476 0.4354755981803515 chr7 159138663 10872796 0.06832278086941072 0.732361440549761 chr8 146364022 5949007 0.04064528234951073 0.4029160389078102 chr9 141213431 10601516 0.07507441696533809 0.5443453484222466 chr10 135534747 14340826 0.10580922101105188 0.5634429247173212 chr11 135006516 836902 0.006198974870220338 0.17446428075932086 chr12 133851895 7370023 0.05506102845985109 0.3180678363390085 chr13 115169878 4666081 0.04051476897457511 0.2578830837756787 chr14 107349540 6676802 0.06219683847737028 0.363607010284404 chr15 102531392 4780116 0.04662099974220578 0.28218085837750206 chr16 90354753 2421239 0.02679702970357298 0.25782908598940196 chr17 81195210 2255031 0.027772956064772786 0.21935293609487777 chr18 78077248 6227049 0.07975497548274242 0.6869454547722709 chr19 59128983 3071841 0.05195152773048709 0.40837774786855846 chr20 63025520 3056622 0.04849816391836196 0.2904275483358385 chr21 48129895 1292414 0.026852624548630327 0.2986298497169842 chr22 51304566 575171 0.011210912494611104 0.12920546989441667 chrMT 16571 87849 5.301369863013699 3.8503183843533857 chrX 155270560 3641232 0.023450884700873108 0.22841883358670942 chrY 59373566 298528 0.005027961433207499 0.2285906380090237