BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506010.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 = 6,020,345 number of mapped reads = 4,428,216 (73.55%) number of supplementary alignments = 261 (0%) number of secondary alignments = 0 number of mapped bases = 207,770,783 bp number of sequenced bases = 207,726,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,948 duplication rate = 7.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1463 >>>>>>> ACTG content number of A's = 60,279,462 bp (29.02%) number of C's = 43,868,453 bp (21.12%) number of T's = 59,558,663 bp (28.67%) number of G's = 44,019,456 bp (21.19%) number of N's = 884 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,014,272 number of insertions = 8,999 mapped reads with insertion percentage = 0.2% number of deletions = 31,127 mapped reads with deletion percentage = 0.7% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.0671X std coverageData = 0.6035X There is a 4.52% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20451121 0.08205043148117172 0.9091949733644246 chr2 243199373 12700582 0.05222292246616935 0.45267204712699716 chr3 198022430 13297986 0.06715393806651095 0.36350030207052714 chr4 191154276 8421976 0.044058527887704695 0.29810748063217124 chr5 180915260 14258767 0.07881461740706672 0.39881032153084967 chr6 171115067 13016464 0.07606848554136966 0.4526619830343543 chr7 159138663 12584654 0.07907980224767881 0.7267032045664004 chr8 146364022 12736992 0.08702269742218481 0.7316460178418852 chr9 141213431 10363168 0.07338656051774566 0.45522057528870735 chr10 135534747 6320903 0.04663677130706564 0.45332609319663775 chr11 135006516 11072293 0.08201302668976362 0.486493971479923 chr12 133851895 6173396 0.04612109525980189 0.30772376572536886 chr13 115169878 5812762 0.0504712004644131 0.314080780680505 chr14 107349540 7794065 0.07260454958633265 1.7501873994742014 chr15 102531392 7195599 0.07017947244878915 0.3741057475811261 chr16 90354753 7476495 0.08274600673193142 0.42596966635677447 chr17 81195210 3587016 0.044177679939493966 0.3155383805346258 chr18 78077248 5726804 0.07334792332844518 0.665201687659207 chr19 59128983 5181746 0.08763462074089791 0.74041612149461 chr20 63025520 5695013 0.09036042860098575 0.4461947679161815 chr21 48129895 3168296 0.06582802642723405 0.3797561612075357 chr22 51304566 1931646 0.0376505670080125 0.2707937431568026 chrMT 16571 30509 1.8411079596886126 1.965425125219617 chrX 155270560 12236816 0.07880963397053505 0.4331951250984059 chrY 59373566 535714 0.009022769493077105 0.14440269086246485