BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617370.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,882,296 (93.38%) number of supplementary alignments = 88,261 (0.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,100,538 number of mapped paired reads (second in pair) = 14,781,758 number of mapped paired reads (both in pair) = 29,174,518 number of mapped paired reads (singletons) = 707,778 number of mapped bases = 2,923,725,708 bp number of sequenced bases = 2,922,861,288 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,554,836 duplication rate = 1.56% >>>>>>> Insert size mean insert size = 65,912.4483 std insert size = 2,455,918.9623 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.3513 >>>>>>> ACTG content number of A's = 883,396,117 bp (30.22%) number of C's = 579,594,617 bp (19.83%) number of T's = 872,957,192 bp (29.87%) number of G's = 586,007,446 bp (20.05%) number of N's = 905,916 bp (0.03%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0135 number of mismatches = 38,570,886 number of insertions = 301,771 mapped reads with insertion percentage = 0.98% number of deletions = 358,908 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 0.9444X std coverageData = 9.375X There is a 52.69% of reference with a coverageData >= 1X There is a 23.58% of reference with a coverageData >= 2X There is a 8.97% of reference with a coverageData >= 3X There is a 3.12% of reference with a coverageData >= 4X There is a 1.06% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% 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 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189733816 0.7612170242095405 19.247118866654446 chr2 243199373 288447851 1.1860550767127183 8.470476327688326 chr3 198022430 232644235 1.1748377948902051 1.4607962315445937 chr4 191154276 159826420 0.8361121882515461 8.68450943348792 chr5 180915260 183506918 1.0143252592401548 1.4566413025050293 chr6 171115067 137333287 0.8025785771395572 3.6246991644897792 chr7 159138663 237342602 1.4914201082611835 10.706069864346029 chr8 146364022 123002667 0.8403886783051097 7.118878666398971 chr9 141213431 123047315 0.8713570241062977 13.908715035206718 chr10 135534747 122685228 0.9051939131151364 19.278364937036123 chr11 135006516 156705757 1.1607273607445732 5.27047734472781 chr12 133851895 129352109 0.9663823511800113 1.483846997675001 chr13 115169878 127124892 1.1038033052357665 1.3021808285651773 chr14 107349540 84821029 0.7901387281212383 1.366538454905087 chr15 102531392 65995135 0.6436578467597514 1.059586962902592 chr16 90354753 73539495 0.8138973607730409 7.6936925925057835 chr17 81195210 91340234 1.124946089800125 6.700557728030814 chr18 78077248 52724666 0.6752884784053864 14.64340580276446 chr19 59128983 54354911 0.9192600353028226 9.172416871879228 chr20 63025520 84045064 1.333508458161075 2.377220993942543 chr21 48129895 46401859 0.9640964103495343 3.187688212416212 chr22 51304566 26097582 0.508679519869635 0.910305286897332 chrMT 16571 1987941 119.96505944119245 19.851871071111695 chrX 155270560 121811670 0.784512337689772 2.882275885769728 chrY 59373566 9853025 0.16594969215761776 7.800528966993521