BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617486.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 = 30,374,919 (94.92%) number of supplementary alignments = 136,059 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,350,082 number of mapped paired reads (second in pair) = 15,024,837 number of mapped paired reads (both in pair) = 29,791,500 number of mapped paired reads (singletons) = 583,419 number of mapped bases = 2,960,218,716 bp number of sequenced bases = 2,958,474,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,203,931 duplication rate = 9.88% >>>>>>> Insert size mean insert size = 29,759.292 std insert size = 1,587,568.4683 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 52.7679 >>>>>>> ACTG content number of A's = 872,445,755 bp (29.49%) number of C's = 598,245,127 bp (20.22%) number of T's = 871,694,776 bp (29.46%) number of G's = 612,654,593 bp (20.71%) number of N's = 3,434,745 bp (0.12%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 36,313,147 number of insertions = 439,028 mapped reads with insertion percentage = 1.42% number of deletions = 1,027,385 mapped reads with deletion percentage = 3.31% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.9562X std coverageData = 9.6611X There is a 38.14% of reference with a coverageData >= 1X There is a 20.57% of reference with a coverageData >= 2X There is a 11.6% of reference with a coverageData >= 3X There is a 6.89% of reference with a coverageData >= 4X There is a 4.24% of reference with a coverageData >= 5X There is a 2.72% of reference with a coverageData >= 6X There is a 1.8% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.86% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% 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 0.02% 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 0.02% 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 0.01% 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 190295929 0.7634722362436963 9.415757499434472 chr2 243199373 305987765 1.2581766195589656 11.374687017883137 chr3 198022430 244769673 1.2360704441411006 2.2381192782739707 chr4 191154276 153159403 0.8012345117511261 6.054226734146912 chr5 180915260 189668859 1.0483850781852233 2.0646938750149433 chr6 171115067 139487113 0.815165580947936 5.3364962008691075 chr7 159138663 228313639 1.4346836569815846 13.091171587882359 chr8 146364022 131120050 0.8958489129247896 3.8155065753454958 chr9 141213431 122374610 0.8665932775190485 18.153308047166934 chr10 135534747 125408535 0.9252869671863555 18.707422199584826 chr11 135006516 167038081 1.237259400131472 12.5829794375037 chr12 133851895 129149075 0.9648654955538731 1.9632010165719218 chr13 115169878 125678251 1.0912423732879182 2.110683519276726 chr14 107349540 86385802 0.8047151576057057 2.2399597700526432 chr15 102531392 66956689 0.6530359892119674 1.4415251922664567 chr16 90354753 79913050 0.8844365940549912 14.884843350030355 chr17 81195210 82698881 1.0185192082143761 13.494677866520172 chr18 78077248 52967381 0.6783971304931239 17.096045455400006 chr19 59128983 35335713 0.5976039364654724 5.768351455364298 chr20 63025520 87408742 1.3868785533225272 2.794011441868691 chr21 48129895 42718866 0.8875744690488105 3.792438499319407 chr22 51304566 22116648 0.4310853735708436 1.2501206719227849 chrMT 16571 2036418 122.89047130529238 93.10116196573168 chrX 155270560 139003954 0.8952370236830471 4.08874871307259 chrY 59373566 10225589 0.17222460581195342 13.715525892130383