BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617673.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 = 29,964,600 (93.64%) number of supplementary alignments = 171,794 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,206,709 number of mapped paired reads (second in pair) = 14,757,891 number of mapped paired reads (both in pair) = 29,125,182 number of mapped paired reads (singletons) = 839,418 number of mapped bases = 2,890,151,681 bp number of sequenced bases = 2,888,406,257 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,830,891 duplication rate = 10.64% >>>>>>> Insert size mean insert size = 47,463.9742 std insert size = 2,040,893.2416 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 52.495 >>>>>>> ACTG content number of A's = 859,515,246 bp (29.76%) number of C's = 574,091,149 bp (19.88%) number of T's = 858,965,770 bp (29.74%) number of G's = 592,835,814 bp (20.52%) number of N's = 2,998,278 bp (0.1%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0158 number of mismatches = 44,660,317 number of insertions = 453,178 mapped reads with insertion percentage = 1.48% number of deletions = 1,057,189 mapped reads with deletion percentage = 3.45% homopolymer indels = 47.6% >>>>>>> Coverage mean coverageData = 0.9336X std coverageData = 10.2891X There is a 33.1% of reference with a coverageData >= 1X There is a 19.05% of reference with a coverageData >= 2X There is a 11.58% of reference with a coverageData >= 3X There is a 7.36% of reference with a coverageData >= 4X There is a 4.83% of reference with a coverageData >= 5X There is a 3.26% of reference with a coverageData >= 6X There is a 2.25% of reference with a coverageData >= 7X There is a 1.6% of reference with a coverageData >= 8X There is a 1.15% of reference with a coverageData >= 9X There is a 0.85% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% 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 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177455369 0.7119555742250288 10.0250548996212 chr2 243199373 298598155 1.2277916316831952 11.836993904196529 chr3 198022430 242031618 1.2222434498960546 2.472595125673929 chr4 191154276 161401540 0.8443522341085375 8.12853772462894 chr5 180915260 191148897 1.0565659137874825 2.31753397962735 chr6 171115067 140335492 0.820123525416964 5.618327419327184 chr7 159138663 226540930 1.4235442583805042 13.178218132611526 chr8 146364022 128501637 0.8779591817994725 4.030230164737437 chr9 141213431 118192559 0.8369781695906815 19.338794593116802 chr10 135534747 122352274 0.9027373179809013 20.956590059514358 chr11 135006516 158908802 1.1770454249778581 11.54348868949086 chr12 133851895 123408691 0.9219794086591004 2.218005409915687 chr13 115169878 124143547 1.077916805642531 2.3074015452343835 chr14 107349540 82755754 0.7708999405120879 2.4432184540762396 chr15 102531392 61679175 0.6015638117933676 1.7619954130886193 chr16 90354753 80152867 0.8870907654409724 16.45039755837619 chr17 81195210 71302772 0.8781647587339204 12.347174751552304 chr18 78077248 53291038 0.6825424738330941 17.93786517035901 chr19 59128983 30848448 0.5217145033595454 5.959202125381002 chr20 63025520 77838227 1.235027128693266 2.9817824751102373 chr21 48129895 42167388 0.876116351386181 4.3140473053136725 chr22 51304566 18731154 0.3650972118154162 1.2735628493844928 chrMT 16571 3051952 184.1742803693199 128.62895206985735 chrX 155270560 143760274 0.9258694887169854 4.280996585589287 chrY 59373566 11553121 0.19458357950068217 16.599779175495154