BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777273.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 49,563,790 number of mapped reads = 49,396,956 (99.66%) number of supplementary alignments = 1,576,556 (3.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,699,705 number of mapped paired reads (second in pair) = 24,697,251 number of mapped paired reads (both in pair) = 49,338,710 number of mapped paired reads (singletons) = 58,246 number of mapped bases = 4,956,266,853 bp number of sequenced bases = 4,955,538,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,866,442 duplication rate = 35.44% >>>>>>> Insert size mean insert size = 438,066.6214 std insert size = 6,524,493.9484 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 54.689 >>>>>>> ACTG content number of A's = 1,384,382,587 bp (27.94%) number of C's = 1,094,538,301 bp (22.09%) number of T's = 1,375,820,590 bp (27.76%) number of G's = 1,100,611,388 bp (22.21%) number of N's = 185,511 bp (0%) GC percentage = 44.3% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 11,413,947 number of insertions = 843,276 mapped reads with insertion percentage = 1.68% number of deletions = 333,431 mapped reads with deletion percentage = 0.67% homopolymer indels = 52.3% >>>>>>> Coverage mean coverageData = 1.601X std coverageData = 13.7134X There is a 22.18% of reference with a coverageData >= 1X There is a 10.89% of reference with a coverageData >= 2X There is a 6.29% of reference with a coverageData >= 3X There is a 4.5% of reference with a coverageData >= 4X There is a 3.56% of reference with a coverageData >= 5X There is a 3.07% of reference with a coverageData >= 6X There is a 2.74% of reference with a coverageData >= 7X There is a 2.52% of reference with a coverageData >= 8X There is a 2.35% of reference with a coverageData >= 9X There is a 2.21% of reference with a coverageData >= 10X There is a 2.09% of reference with a coverageData >= 11X There is a 1.99% of reference with a coverageData >= 12X There is a 1.9% of reference with a coverageData >= 13X There is a 1.82% of reference with a coverageData >= 14X There is a 1.75% of reference with a coverageData >= 15X There is a 1.69% of reference with a coverageData >= 16X There is a 1.63% of reference with a coverageData >= 17X There is a 1.57% of reference with a coverageData >= 18X There is a 1.52% of reference with a coverageData >= 19X There is a 1.47% of reference with a coverageData >= 20X There is a 1.42% of reference with a coverageData >= 21X There is a 1.38% of reference with a coverageData >= 22X There is a 1.34% of reference with a coverageData >= 23X There is a 1.3% of reference with a coverageData >= 24X There is a 1.26% of reference with a coverageData >= 25X There is a 1.23% of reference with a coverageData >= 26X There is a 1.2% of reference with a coverageData >= 27X There is a 1.17% of reference with a coverageData >= 28X There is a 1.13% of reference with a coverageData >= 29X There is a 1.11% of reference with a coverageData >= 30X There is a 1.08% of reference with a coverageData >= 31X There is a 1.05% of reference with a coverageData >= 32X There is a 1.03% of reference with a coverageData >= 33X There is a 1% of reference with a coverageData >= 34X There is a 0.98% of reference with a coverageData >= 35X There is a 0.96% of reference with a coverageData >= 36X There is a 0.93% of reference with a coverageData >= 37X There is a 0.91% of reference with a coverageData >= 38X There is a 0.89% of reference with a coverageData >= 39X There is a 0.87% of reference with a coverageData >= 40X There is a 0.85% of reference with a coverageData >= 41X There is a 0.84% of reference with a coverageData >= 42X There is a 0.82% of reference with a coverageData >= 43X There is a 0.8% of reference with a coverageData >= 44X There is a 0.79% of reference with a coverageData >= 45X There is a 0.77% of reference with a coverageData >= 46X There is a 0.75% of reference with a coverageData >= 47X There is a 0.74% of reference with a coverageData >= 48X There is a 0.72% of reference with a coverageData >= 49X There is a 0.71% of reference with a coverageData >= 50X There is a 0.7% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 492845102 1.977307418624245 15.824937941043903 chr2 243199373 443047478 1.8217459713598851 14.393598021229622 chr3 198022430 308837393 1.559608136310619 13.518796509680922 chr4 191154276 234405615 1.2262640413024295 11.330078497674396 chr5 180915260 263784801 1.4580572197171207 12.217275034166114 chr6 171115067 233389626 1.363933814197671 11.968366413760473 chr7 159138663 323739218 2.0343215903479095 16.684561003869913 chr8 146364022 178571635 1.2200514344980216 12.039185111773305 chr9 141213431 171220019 1.2124910342274737 11.222967888100262 chr10 135534747 207347494 1.5298475010249586 12.442027052677595 chr11 135006516 337975340 2.5034002062537484 19.0022282176981 chr12 133851895 279408263 2.0874434612972794 15.921647451558343 chr13 115169878 157331629 1.3660831437192285 13.765422525923105 chr14 107349540 111241898 1.0362587301259045 9.49309825864527 chr15 102531392 229436658 2.2377210874109656 17.546005521925863 chr16 90354753 142380043 1.5757891895294096 12.482151669634655 chr17 81195210 204200792 2.514936435289717 16.891692147576723 chr18 78077248 78566610 1.0062676645570294 9.340966510560015 chr19 59128983 214672947 3.6305875073143064 22.00914865196689 chr20 63025520 124757749 1.9794798837042518 14.65800970951848 chr21 48129895 32779967 0.6810728965853758 8.128036034950346 chr22 51304566 48130103 0.9381251368542909 8.868974332336068 chrMT 16571 1658322 100.0737432864643 28.889391081545703 chrX 155270560 135197807 0.8707240252112184 8.942458421403991 chrY 59373566 1340344 0.022574759952939328 0.6168155265230589