BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926984.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 34,190,246 number of mapped reads = 33,677,771 (98.5%) number of supplementary alignments = 633,024 (1.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,907,655 number of mapped paired reads (second in pair) = 16,770,116 number of mapped paired reads (both in pair) = 33,368,732 number of mapped paired reads (singletons) = 309,039 number of mapped bases = 3,200,492,351 bp number of sequenced bases = 3,198,085,662 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,608,739 duplication rate = 5.96% >>>>>>> Insert size mean insert size = 175,242.9796 std insert size = 4,090,135.2617 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 53.2883 >>>>>>> ACTG content number of A's = 904,739,869 bp (28.29%) number of C's = 657,418,215 bp (20.56%) number of T's = 915,953,845 bp (28.64%) number of G's = 719,719,691 bp (22.5%) number of N's = 254,042 bp (0.01%) GC percentage = 43.06% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 29,765,018 number of insertions = 514,262 mapped reads with insertion percentage = 1.5% number of deletions = 1,688,598 mapped reads with deletion percentage = 4.88% homopolymer indels = 52.55% >>>>>>> Coverage mean coverageData = 1.0339X std coverageData = 4.2258X There is a 35.91% of reference with a coverageData >= 1X There is a 21.9% of reference with a coverageData >= 2X There is a 13.57% of reference with a coverageData >= 3X There is a 8.92% of reference with a coverageData >= 4X There is a 6.01% of reference with a coverageData >= 5X There is a 4.16% of reference with a coverageData >= 6X There is a 2.93% of reference with a coverageData >= 7X There is a 2.09% of reference with a coverageData >= 8X There is a 1.52% of reference with a coverageData >= 9X There is a 1.11% of reference with a coverageData >= 10X There is a 0.82% of reference with a coverageData >= 11X There is a 0.62% of reference with a coverageData >= 12X There is a 0.46% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.21% 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 0.1% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% 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 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 262956004 1.0549863544773275 4.896763231356775 chr2 243199373 278659543 1.145806995974451 7.3890741204666135 chr3 198022430 216539268 1.0935087908980816 2.1732591051486754 chr4 191154276 190639469 0.9973068507240717 3.218858781514578 chr5 180915260 190584831 1.053448067343794 2.099272110174728 chr6 171115067 184178826 1.0763448785021368 3.7999840566983853 chr7 159138663 163409847 1.0268393859762415 3.2331125287951568 chr8 146364022 163057962 1.114057674638102 2.70300215487354 chr9 141213431 136989392 0.9700875549153678 5.160458908155459 chr10 135534747 159168576 1.174374686367327 6.3629378541938895 chr11 135006516 157339655 1.1654226748581529 6.193721664795211 chr12 133851895 140398312 1.048907914228633 2.59408096539323 chr13 115169878 94164131 0.8176107558262761 1.9411013336486258 chr14 107349540 95193686 0.8867637998262499 2.0409566514095214 chr15 102531392 96538643 0.941552056564296 2.17675035986409 chr16 90354753 101927597 1.1280822935789554 6.033768093118212 chr17 81195210 83720147 1.0310971176747987 3.054706511592473 chr18 78077248 85280880 1.0922628830360415 5.7629700910759745 chr19 59128983 52579164 0.8892282825158687 3.038823528904976 chr20 63025520 77441118 1.228726363542895 2.555532029506939 chr21 48129895 41195380 0.8559208367273604 3.4374979598216346 chr22 51304566 42763117 0.8335148376462244 2.121610113111912 chrMT 16571 8412 0.5076338181159857 1.8138225661816536 chrX 155270560 180208011 1.160606434342737 3.0473535012676902 chrY 59373566 5550380 0.09348234195668827 2.880556592184754