BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504634.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 = 348,638,182 number of mapped reads = 302,930,289 (86.89%) number of supplementary alignments = 3,303,690 (0.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 151,960,395 number of mapped paired reads (second in pair) = 150,969,894 number of mapped paired reads (both in pair) = 300,568,354 number of mapped paired reads (singletons) = 2,361,935 number of mapped bases = 29,890,493,025 bp number of sequenced bases = 29,883,305,132 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,616,276 duplication rate = 25.42% >>>>>>> Insert size mean insert size = 40,155.0135 std insert size = 1,915,618.442 median insert size = 367 >>>>>>> Mapping quality mean mapping quality = 53.6247 >>>>>>> ACTG content number of A's = 7,517,269,528 bp (25.16%) number of C's = 7,321,306,148 bp (24.5%) number of T's = 7,555,255,299 bp (25.28%) number of G's = 7,478,630,703 bp (25.03%) number of N's = 10,843,454 bp (0.04%) GC percentage = 49.53% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 204,365,850 number of insertions = 2,411,584 mapped reads with insertion percentage = 0.78% number of deletions = 2,884,652 mapped reads with deletion percentage = 0.92% homopolymer indels = 38.89% >>>>>>> Coverage mean coverageData = 9.6555X std coverageData = 38.0178X There is a 62.46% of reference with a coverageData >= 1X There is a 51.57% of reference with a coverageData >= 2X There is a 44.2% of reference with a coverageData >= 3X There is a 38.75% of reference with a coverageData >= 4X There is a 34.43% of reference with a coverageData >= 5X There is a 30.93% of reference with a coverageData >= 6X There is a 28.02% of reference with a coverageData >= 7X There is a 25.56% of reference with a coverageData >= 8X There is a 23.46% of reference with a coverageData >= 9X There is a 21.65% of reference with a coverageData >= 10X There is a 20.07% of reference with a coverageData >= 11X There is a 18.68% of reference with a coverageData >= 12X There is a 17.45% of reference with a coverageData >= 13X There is a 16.35% of reference with a coverageData >= 14X There is a 15.36% of reference with a coverageData >= 15X There is a 14.47% of reference with a coverageData >= 16X There is a 13.67% of reference with a coverageData >= 17X There is a 12.94% of reference with a coverageData >= 18X There is a 12.27% of reference with a coverageData >= 19X There is a 11.66% of reference with a coverageData >= 20X There is a 11.1% of reference with a coverageData >= 21X There is a 10.58% of reference with a coverageData >= 22X There is a 10.11% of reference with a coverageData >= 23X There is a 9.66% of reference with a coverageData >= 24X There is a 9.25% of reference with a coverageData >= 25X There is a 8.87% of reference with a coverageData >= 26X There is a 8.51% of reference with a coverageData >= 27X There is a 8.17% of reference with a coverageData >= 28X There is a 7.86% of reference with a coverageData >= 29X There is a 7.56% of reference with a coverageData >= 30X There is a 7.28% of reference with a coverageData >= 31X There is a 7.02% of reference with a coverageData >= 32X There is a 6.77% of reference with a coverageData >= 33X There is a 6.54% of reference with a coverageData >= 34X There is a 6.32% of reference with a coverageData >= 35X There is a 6.11% of reference with a coverageData >= 36X There is a 5.91% of reference with a coverageData >= 37X There is a 5.72% of reference with a coverageData >= 38X There is a 5.54% of reference with a coverageData >= 39X There is a 5.37% of reference with a coverageData >= 40X There is a 5.21% of reference with a coverageData >= 41X There is a 5.05% of reference with a coverageData >= 42X There is a 4.9% of reference with a coverageData >= 43X There is a 4.76% of reference with a coverageData >= 44X There is a 4.63% of reference with a coverageData >= 45X There is a 4.49% of reference with a coverageData >= 46X There is a 4.37% of reference with a coverageData >= 47X There is a 4.25% of reference with a coverageData >= 48X There is a 4.14% of reference with a coverageData >= 49X There is a 4.03% of reference with a coverageData >= 50X There is a 3.92% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2873304878 11.52777419960771 37.32752452384984 chr2 243199373 2424499178 9.969183506077542 29.1951372417463 chr3 198022430 1416719303 7.154337531359452 24.208012416687804 chr4 191154276 926313703 4.845895798846791 15.044736919020622 chr5 180915260 2014055469 11.132590302222157 31.478025869402707 chr6 171115067 861129011 5.03245579771184 18.429472818293636 chr7 159138663 2057393786 12.928308854775285 33.10798126340707 chr8 146364022 1591418298 10.873015624017219 28.400816245822913 chr9 141213431 1036285540 7.338434684729103 70.71553851645149 chr10 135534747 1212944181 8.949322648604642 28.43256936016547 chr11 135006516 1397179423 10.348977696750577 35.3892792242825 chr12 133851895 1258275727 9.40050738168481 27.844538137361074 chr13 115169878 138198799 1.1999561117881883 5.578921038305326 chr14 107349540 922110977 8.589799052702043 23.200195276234414 chr15 102531392 1088817235 10.619354850853874 29.781080782376456 chr16 90354753 1934150845 21.406188172524804 53.25762309964921 chr17 81195210 1292270553 15.91560084640461 41.7479554669286 chr18 78077248 513229236 6.573352021833556 72.7405450556073 chr19 59128983 1619826690 27.39480044836895 113.00741106258265 chr20 63025520 1020880525 16.19789134623562 48.87886283356611 chr21 48129895 320051438 6.649743117037758 21.656620042303686 chr22 51304566 748409418 14.587579164006572 35.87140209386462 chrMT 16571 2933497 177.02594894695554 68.7868719687551 chrX 155270560 1175620731 7.571433573756673 18.245115997337162 chrY 59373566 44474584 0.7490637163346395 33.25266522843477