BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053679.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,226,145 number of mapped reads = 6,783,497 (82.46%) number of supplementary alignments = 401 (0%) number of secondary alignments = 0 number of mapped bases = 318,649,328 bp number of sequenced bases = 318,579,667 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,086,228 duplication rate = 12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7236 >>>>>>> ACTG content number of A's = 95,380,300 bp (29.94%) number of C's = 60,917,945 bp (19.12%) number of T's = 96,523,194 bp (30.3%) number of G's = 65,742,671 bp (20.64%) number of N's = 15,557 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,501,988 number of insertions = 13,844 mapped reads with insertion percentage = 0.2% number of deletions = 46,520 mapped reads with deletion percentage = 0.68% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.1029X std coverageData = 0.6781X There is a 5.5% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 26077473 0.10462350262308875 0.7885238816817971 chr2 243199373 34520529 0.14194333058580705 0.8234049564680175 chr3 198022430 20863522 0.10535938782288451 0.6313233299936574 chr4 191154276 16101005 0.08423042024966264 0.5715229807364336 chr5 180915260 15776863 0.08720581669009016 0.553417645028291 chr6 171115067 21239632 0.12412484985907173 0.7541848040335037 chr7 159138663 16426697 0.10322253995561091 0.6883924676817242 chr8 146364022 20106294 0.13737183308613915 0.7955139204249817 chr9 141213431 16652474 0.11792415127991614 0.7110419423752197 chr10 135534747 10774535 0.07949647775562675 0.67002956159135 chr11 135006516 14950033 0.11073564034494454 0.6867091504944209 chr12 133851895 16463464 0.12299761613386198 0.7012724081126962 chr13 115169878 9109615 0.07909720109280657 0.5483449932040484 chr14 107349540 6359659 0.05924253611147286 0.5075632129779772 chr15 102531392 6753095 0.06586368202238004 0.4744915743196227 chr16 90354753 7048985 0.07801454562108094 0.556428513190344 chr17 81195210 6586799 0.08112299974345777 0.536834517019931 chr18 78077248 9532172 0.12208642394772931 0.801444896127984 chr19 59128983 5803347 0.09814724870204515 0.7191692050543134 chr20 63025520 6420553 0.1018722733267413 0.6325917118791019 chr21 48129895 3579456 0.07437074192661339 0.5626706960309998 chr22 51304566 4194868 0.08176402856619039 0.5583613433413106 chrMT 16571 37178 2.24355802305232 3.5315543659473083 chrX 155270560 22546622 0.14520860876652986 0.8031055608757857 chrY 59373566 724458 0.012201692584878597 0.2357023812704335