BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153348.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 42,426,706 number of mapped reads = 42,165,874 (99.39%) number of supplementary alignments = 278,325 (0.66%) number of secondary alignments = 0 number of mapped bases = 3,742,616,501 bp number of sequenced bases = 3,742,027,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,824,732 duplication rate = 44.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.005 >>>>>>> ACTG content number of A's = 994,305,208 bp (26.57%) number of C's = 881,598,513 bp (23.56%) number of T's = 1,019,804,477 bp (27.25%) number of G's = 845,275,470 bp (22.59%) number of N's = 1,044,112 bp (0.03%) GC percentage = 46.15% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 8,274,116 number of insertions = 378,424 mapped reads with insertion percentage = 0.89% number of deletions = 288,540 mapped reads with deletion percentage = 0.68% homopolymer indels = 48.98% >>>>>>> Coverage mean coverageData = 1.209X std coverageData = 14.9324X There is a 12.94% of reference with a coverageData >= 1X There is a 8.73% of reference with a coverageData >= 2X There is a 3.89% of reference with a coverageData >= 3X There is a 3.11% of reference with a coverageData >= 4X There is a 2.25% of reference with a coverageData >= 5X There is a 1.99% of reference with a coverageData >= 6X There is a 1.76% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.52% of reference with a coverageData >= 9X There is a 1.44% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.32% of reference with a coverageData >= 12X There is a 1.26% of reference with a coverageData >= 13X There is a 1.22% of reference with a coverageData >= 14X There is a 1.17% of reference with a coverageData >= 15X There is a 1.14% of reference with a coverageData >= 16X There is a 1.1% of reference with a coverageData >= 17X There is a 1.07% of reference with a coverageData >= 18X There is a 1.03% of reference with a coverageData >= 19X There is a 1% of reference with a coverageData >= 20X There is a 0.98% of reference with a coverageData >= 21X There is a 0.95% of reference with a coverageData >= 22X There is a 0.92% of reference with a coverageData >= 23X There is a 0.9% of reference with a coverageData >= 24X There is a 0.88% of reference with a coverageData >= 25X There is a 0.86% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.82% of reference with a coverageData >= 28X There is a 0.8% of reference with a coverageData >= 29X There is a 0.78% of reference with a coverageData >= 30X There is a 0.76% of reference with a coverageData >= 31X There is a 0.75% of reference with a coverageData >= 32X There is a 0.73% of reference with a coverageData >= 33X There is a 0.71% of reference with a coverageData >= 34X There is a 0.7% of reference with a coverageData >= 35X There is a 0.68% of reference with a coverageData >= 36X There is a 0.67% of reference with a coverageData >= 37X There is a 0.66% of reference with a coverageData >= 38X There is a 0.64% of reference with a coverageData >= 39X There is a 0.63% of reference with a coverageData >= 40X There is a 0.62% of reference with a coverageData >= 41X There is a 0.61% of reference with a coverageData >= 42X There is a 0.6% of reference with a coverageData >= 43X There is a 0.59% of reference with a coverageData >= 44X There is a 0.57% of reference with a coverageData >= 45X There is a 0.56% of reference with a coverageData >= 46X There is a 0.55% of reference with a coverageData >= 47X There is a 0.54% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.53% of reference with a coverageData >= 50X There is a 0.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 393384404 1.5782685010842963 18.745928011928193 chr2 243199373 264672277 1.088293418420943 12.07621336622879 chr3 198022430 194844059 0.9839494394650141 11.080587136166784 chr4 191154276 161312687 0.8438874106064989 12.040739856995136 chr5 180915260 247404269 1.367514652992788 16.303201122197105 chr6 171115067 127033520 0.7423865252029501 9.325171678774643 chr7 159138663 192607902 1.2103149440183496 16.92050023821325 chr8 146364022 232277711 1.586986390685547 21.033555383920692 chr9 141213431 99911813 0.7075234437154919 10.172443417225727 chr10 135534747 185191067 1.3663733551662587 14.742925039498239 chr11 135006516 171186229 1.2679849393343354 14.04447076349651 chr12 133851895 177989420 1.3297489736697414 15.15003819953548 chr13 115169878 52741325 0.4579437428943009 8.542082954219428 chr14 107349540 108588810 1.0115442506786707 12.147836836574067 chr15 102531392 172255778 1.6800296439942999 18.8057755185196 chr16 90354753 172859843 1.9131239615031652 19.68078051797928 chr17 81195210 158836840 1.9562341177515274 18.7897939993226 chr18 78077248 43197870 0.5532709093435261 7.693770351178503 chr19 59128983 176355965 2.9825638130796195 24.486099526504056 chr20 63025520 83662589 1.3274398846689404 14.176459496779959 chr21 48129895 37296368 0.7749106454522704 10.001293911907734 chr22 51304566 48605110 0.9473837084987718 13.1569377140563 chrMT 16571 1057 0.06378613239997587 0.3750328877673643 chrX 155270560 237558455 1.5299645663672494 17.74723608689762 chrY 59373566 2841133 0.04785181674956158 2.191005876444299