BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618673.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 209,057,054 number of mapped reads = 202,780,800 (97%) number of supplementary alignments = 514,751 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 101,345,773 number of mapped paired reads (second in pair) = 101,435,027 number of mapped paired reads (both in pair) = 200,093,534 number of mapped paired reads (singletons) = 2,687,266 number of mapped bases = 19,644,190,106 bp number of sequenced bases = 19,638,627,619 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,198,206 duplication rate = 10.46% >>>>>>> Insert size mean insert size = 37,986.1041 std insert size = 1,866,846.0511 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 53.6144 >>>>>>> ACTG content number of A's = 5,741,177,879 bp (29.23%) number of C's = 4,102,007,878 bp (20.89%) number of T's = 5,713,993,643 bp (29.1%) number of G's = 4,080,641,452 bp (20.78%) number of N's = 806,767 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 208,936,383 number of insertions = 2,221,269 mapped reads with insertion percentage = 1.07% number of deletions = 2,457,685 mapped reads with deletion percentage = 1.18% homopolymer indels = 41.22% >>>>>>> Coverage mean coverageData = 6.3456X std coverageData = 60.0629X There is a 91.05% of reference with a coverageData >= 1X There is a 89.24% of reference with a coverageData >= 2X There is a 85.14% of reference with a coverageData >= 3X There is a 78% of reference with a coverageData >= 4X There is a 67.96% of reference with a coverageData >= 5X There is a 56.04% of reference with a coverageData >= 6X There is a 43.69% of reference with a coverageData >= 7X There is a 32.27% of reference with a coverageData >= 8X There is a 22.66% of reference with a coverageData >= 9X There is a 15.2% of reference with a coverageData >= 10X There is a 9.8% of reference with a coverageData >= 11X There is a 6.12% of reference with a coverageData >= 12X There is a 3.75% of reference with a coverageData >= 13X There is a 2.28% of reference with a coverageData >= 14X There is a 1.4% of reference with a coverageData >= 15X There is a 0.89% of reference with a coverageData >= 16X There is a 0.6% of reference with a coverageData >= 17X There is a 0.43% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% 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 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1598141970 6.411787315065506 150.101677141224 chr2 243199373 1660885307 6.8293157441651795 35.17198306354356 chr3 198022430 1289075460 6.509744678923494 4.374578340983299 chr4 191154276 1299755984 6.7995129965075956 51.14386340773847 chr5 180915260 1173289792 6.4853003113170224 5.08434731133599 chr6 171115067 1130850896 6.608716086935816 40.317160717100585 chr7 159138663 1057802962 6.647051961219506 45.62759409637454 chr8 146364022 976416104 6.671148350924655 36.57221641472697 chr9 141213431 831208635 5.886186810374999 60.47796326989341 chr10 135534747 1013271667 7.476102545128151 124.19147216410063 chr11 135006516 893149604 6.615603679454997 27.80169759289383 chr12 133851895 865350308 6.464983614912587 5.395713635064463 chr13 115169878 622867299 5.408248318193061 4.075454313360292 chr14 107349540 588582037 5.482855697378862 5.4193841919905035 chr15 102531392 553403044 5.397401061325686 4.088112441096342 chr16 90354753 606394784 6.711266024931748 37.5587890358696 chr17 81195210 547123336 6.738369615646046 30.788854436935505 chr18 78077248 549211834 7.034210965017619 87.59899426580138 chr19 59128983 394201200 6.666801625862566 62.18930450850338 chr20 63025520 410707761 6.5165310972444175 15.757533329557813 chr21 48129895 268410549 5.576794817441426 18.345800269520737 chr22 51304566 240182501 4.681503416284625 4.88336201534911 chrMT 16571 5792536 349.558626516203 44.029028040846164 chrX 155270560 1010493926 6.507955700037406 16.30212210019522 chrY 59373566 57620610 0.9704758174706906 41.94675833154315