BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089594.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 = 17,863,389 number of mapped reads = 14,893,688 (83.38%) number of supplementary alignments = 597 (0%) number of secondary alignments = 0 number of mapped bases = 702,746,649 bp number of sequenced bases = 702,614,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,350,042 duplication rate = 14.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6742 >>>>>>> ACTG content number of A's = 204,193,473 bp (29.06%) number of C's = 147,543,783 bp (21%) number of T's = 201,461,173 bp (28.67%) number of G's = 149,371,891 bp (21.26%) number of N's = 43,781 bp (0.01%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 3,965,139 number of insertions = 28,532 mapped reads with insertion percentage = 0.19% number of deletions = 88,595 mapped reads with deletion percentage = 0.59% homopolymer indels = 44.8% >>>>>>> Coverage mean coverageData = 0.227X std coverageData = 1.452X There is a 8.99% of reference with a coverageData >= 1X There is a 4.42% of reference with a coverageData >= 2X There is a 2.65% of reference with a coverageData >= 3X There is a 1.73% of reference with a coverageData >= 4X There is a 1.19% of reference with a coverageData >= 5X There is a 0.84% of reference with a coverageData >= 6X There is a 0.6% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 56697494 0.22747182643930103 2.0328707598343585 chr2 243199373 59487500 0.2446038378561116 1.781184893163551 chr3 198022430 46107258 0.232838562783014 1.1073865533912601 chr4 191154276 44546853 0.23304136288324515 1.1783066390688857 chr5 180915260 43799863 0.24210153969322434 1.1259838814710068 chr6 171115067 40213797 0.23501026359063987 1.2807517878373507 chr7 159138663 38514223 0.2420167561669159 1.8600950002700405 chr8 146364022 35626984 0.24341353505576666 1.6741340887642324 chr9 141213431 30118023 0.21328015888233748 1.3373738566218456 chr10 135534747 33559573 0.24760862983718854 1.5261682143043027 chr11 135006516 32028753 0.23723857150717081 1.4337075434387643 chr12 133851895 32144737 0.24015152717860289 1.1580950910844625 chr13 115169878 21704419 0.18845569151336602 0.9979591250636171 chr14 107349540 21318815 0.1985925137639155 1.2416955839172703 chr15 102531392 19834825 0.19345124076731543 1.008502138155143 chr16 90354753 20016029 0.2215271287388722 1.1764258949876143 chr17 81195210 18459854 0.22735151494774136 1.2428064168992854 chr18 78077248 18456313 0.23638529114140908 2.027233136112967 chr19 59128983 13713495 0.23192509500797603 2.01281144861469 chr20 63025520 15057139 0.23890543068902884 1.2109240107774002 chr21 48129895 9262632 0.19245070033915512 1.1490230923546485 chr22 51304566 8109605 0.15806789984345643 0.9144288093756158 chrMT 16571 205823 12.420674672620844 11.09200464702305 chrX 155270560 41632491 0.2681286845362057 1.3721822012500207 chrY 59373566 2130151 0.03587709385688574 0.6650035723546481