BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617401.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 = 28,157,403 (87.99%) number of supplementary alignments = 427,197 (1.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,301,843 number of mapped paired reads (second in pair) = 13,855,560 number of mapped paired reads (both in pair) = 27,308,818 number of mapped paired reads (singletons) = 848,585 number of mapped bases = 2,757,251,102 bp number of sequenced bases = 2,756,654,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,243,324 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 58,139.1321 std insert size = 2,313,421.7792 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.6801 >>>>>>> ACTG content number of A's = 826,322,836 bp (29.98%) number of C's = 550,566,789 bp (19.97%) number of T's = 816,118,230 bp (29.61%) number of G's = 563,391,873 bp (20.44%) number of N's = 254,944 bp (0.01%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0143 number of mismatches = 38,838,011 number of insertions = 248,465 mapped reads with insertion percentage = 0.87% number of deletions = 266,949 mapped reads with deletion percentage = 0.93% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.8907X std coverageData = 2.7391X There is a 28.67% of reference with a coverageData >= 1X There is a 16.2% of reference with a coverageData >= 2X There is a 10.22% of reference with a coverageData >= 3X There is a 6.99% of reference with a coverageData >= 4X There is a 5.03% of reference with a coverageData >= 5X There is a 3.75% of reference with a coverageData >= 6X There is a 2.88% of reference with a coverageData >= 7X There is a 2.27% of reference with a coverageData >= 8X There is a 1.81% of reference with a coverageData >= 9X There is a 1.47% of reference with a coverageData >= 10X There is a 1.21% of reference with a coverageData >= 11X There is a 1.01% of reference with a coverageData >= 12X There is a 0.85% of reference with a coverageData >= 13X There is a 0.72% of reference with a coverageData >= 14X There is a 0.62% of reference with a coverageData >= 15X There is a 0.54% of reference with a coverageData >= 16X There is a 0.46% of reference with a coverageData >= 17X There is a 0.41% of reference with a coverageData >= 18X There is a 0.36% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% 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 177364429 0.7115907205703612 2.5706051539176773 chr2 243199373 275156769 1.1314041052235773 2.917359613903063 chr3 198022430 233446381 1.1788885784302314 3.185123656652051 chr4 191154276 133503684 0.6984080439822334 2.1547866585794875 chr5 180915260 176984183 0.9782711696072515 2.700611195012712 chr6 171115067 126956616 0.7419370966321744 2.440280780148743 chr7 159138663 206870507 1.2999387018854116 3.04192161481556 chr8 146364022 122280272 0.8354530732969336 3.0291037134114696 chr9 141213431 110307918 0.781143246919622 2.4489449965802823 chr10 135534747 88226551 0.6509515305326095 2.256874135805987 chr11 135006516 204203749 1.5125473573438486 3.572310998151832 chr12 133851895 131342313 0.9812510536365585 2.6291659352292944 chr13 115169878 120030836 1.0422068520381693 2.6039193404319283 chr14 107349540 79807993 0.7434404749195944 2.698982186197768 chr15 102531392 63164941 0.6160546518279982 2.239993315229868 chr16 90354753 68567755 0.7588726959388622 3.074419056205806 chr17 81195210 83891985 1.0332134740460674 3.4554725739194883 chr18 78077248 39666110 0.5080367330569848 1.8750044874983767 chr19 59128983 38735869 0.6551079865520434 2.1549597032959866 chr20 63025520 93230229 1.4792456928558464 4.35038810607903 chr21 48129895 37902911 0.7875128545366659 2.358653282779363 chr22 51304566 21927900 0.4274064027751448 1.9260091098447087 chrMT 16571 167099 10.083821133305172 5.161086158991826 chrX 155270560 121301677 0.7812277936010535 2.407924870329364 chrY 59373566 2212425 0.037262794692169914 0.5882658790970674