BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975269.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 68,138,936 number of mapped reads = 68,004,775 (99.8%) number of supplementary alignments = 118,757 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 34,018,133 number of mapped paired reads (second in pair) = 33,986,642 number of mapped paired reads (both in pair) = 67,939,542 number of mapped paired reads (singletons) = 65,233 number of mapped bases = 6,302,538,213 bp number of sequenced bases = 6,300,547,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,144,208 duplication rate = 42.93% >>>>>>> Insert size mean insert size = 81,446.6448 std insert size = 2,822,645.4868 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 56.0633 >>>>>>> ACTG content number of A's = 1,630,657,605 bp (25.88%) number of C's = 1,440,455,410 bp (22.86%) number of T's = 1,697,096,777 bp (26.94%) number of G's = 1,532,061,889 bp (24.32%) number of N's = 275,361 bp (0%) GC percentage = 47.18% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 37,308,943 number of insertions = 499,667 mapped reads with insertion percentage = 0.73% number of deletions = 1,378,124 mapped reads with deletion percentage = 2% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 2.0359X std coverageData = 23.9902X There is a 15.91% of reference with a coverageData >= 1X There is a 8% of reference with a coverageData >= 2X There is a 4.67% of reference with a coverageData >= 3X There is a 3.49% of reference with a coverageData >= 4X There is a 2.82% of reference with a coverageData >= 5X There is a 2.48% of reference with a coverageData >= 6X There is a 2.26% of reference with a coverageData >= 7X There is a 2.11% of reference with a coverageData >= 8X There is a 1.99% of reference with a coverageData >= 9X There is a 1.9% of reference with a coverageData >= 10X There is a 1.83% of reference with a coverageData >= 11X There is a 1.76% of reference with a coverageData >= 12X There is a 1.7% of reference with a coverageData >= 13X There is a 1.65% of reference with a coverageData >= 14X There is a 1.6% of reference with a coverageData >= 15X There is a 1.56% of reference with a coverageData >= 16X There is a 1.52% of reference with a coverageData >= 17X There is a 1.48% of reference with a coverageData >= 18X There is a 1.45% of reference with a coverageData >= 19X There is a 1.41% of reference with a coverageData >= 20X There is a 1.38% of reference with a coverageData >= 21X There is a 1.35% of reference with a coverageData >= 22X There is a 1.32% of reference with a coverageData >= 23X There is a 1.3% of reference with a coverageData >= 24X There is a 1.27% of reference with a coverageData >= 25X There is a 1.25% of reference with a coverageData >= 26X There is a 1.22% of reference with a coverageData >= 27X There is a 1.2% of reference with a coverageData >= 28X There is a 1.18% of reference with a coverageData >= 29X There is a 1.16% of reference with a coverageData >= 30X There is a 1.14% of reference with a coverageData >= 31X There is a 1.12% of reference with a coverageData >= 32X There is a 1.1% of reference with a coverageData >= 33X There is a 1.08% of reference with a coverageData >= 34X There is a 1.06% of reference with a coverageData >= 35X There is a 1.05% of reference with a coverageData >= 36X There is a 1.03% of reference with a coverageData >= 37X There is a 1.01% of reference with a coverageData >= 38X There is a 1% of reference with a coverageData >= 39X There is a 0.98% of reference with a coverageData >= 40X There is a 0.97% of reference with a coverageData >= 41X There is a 0.96% of reference with a coverageData >= 42X There is a 0.94% of reference with a coverageData >= 43X There is a 0.93% of reference with a coverageData >= 44X There is a 0.92% of reference with a coverageData >= 45X There is a 0.9% of reference with a coverageData >= 46X There is a 0.89% of reference with a coverageData >= 47X There is a 0.88% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.86% of reference with a coverageData >= 50X There is a 0.84% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 743551354 2.9831474482063576 31.23257814839057 chr2 243199373 445327219 1.8311199305600183 20.630139885672563 chr3 198022430 412982840 2.0855356638134377 24.3463275670607 chr4 191154276 266842559 1.3959539100239642 18.247159092676252 chr5 180915260 301151295 1.6645986358475233 20.4611077246572 chr6 171115067 569002909 3.325264799738529 41.700354088243486 chr7 159138663 325987236 2.0484477489923365 24.718465007931425 chr8 146364022 218538290 1.493114817519841 18.006341904484096 chr9 141213431 258526442 1.83074966856375 21.49167272970879 chr10 135534747 276330761 2.0388185842852535 22.255459559443935 chr11 135006516 292330828 2.1653090284916323 22.564933830965092 chr12 133851895 338904816 2.5319388716909836 24.805085594209242 chr13 115169878 121789579 1.0574777113161482 16.619736596758756 chr14 107349540 206258898 1.9213766356148336 21.98192193045516 chr15 102531392 217498795 2.1212897899601324 22.695384366350233 chr16 90354753 206347553 2.2837487364942497 23.575561962804258 chr17 81195210 246979302 3.0417964557268835 26.071435763956444 chr18 78077248 114457946 1.4659577396990222 19.36258671175204 chr19 59128983 243952474 4.125768136414591 32.03506906684677 chr20 63025520 167699103 2.6608126834970975 28.74280925295686 chr21 48129895 62525075 1.2990902016304005 17.54775759124833 chr22 51304566 112907487 2.2007297946931272 24.038223972930968 chrMT 16571 106351 6.417898738760485 11.543292298580534 chrX 155270560 140247807 0.90324789837816 11.769425040847043 chrY 59373566 12291294 0.20701626713814023 4.134353667777808