BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708578.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,839,176 number of mapped reads = 3,753,335 (97.76%) number of supplementary alignments = 105 (0%) number of secondary alignments = 0 number of mapped bases = 187,195,439 bp number of sequenced bases = 187,179,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,974 duplication rate = 0.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6647 >>>>>>> ACTG content number of A's = 58,046,252 bp (31.01%) number of C's = 35,422,150 bp (18.92%) number of T's = 57,715,234 bp (30.83%) number of G's = 35,989,470 bp (19.23%) number of N's = 6,421 bp (0%) GC percentage = 38.15% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 276,396 number of insertions = 12,023 mapped reads with insertion percentage = 0.32% number of deletions = 9,471 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 0.2544X There is a 5.68% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 14605363 0.05859709773802329 0.2516865219655681 chr2 243199373 17028500 0.07001868380639287 0.2730346286781466 chr3 198022430 13653634 0.068949936630916 0.27042914767316 chr4 191154276 14819164 0.07752462728063693 0.2864697910217532 chr5 180915260 12775303 0.07061484476212786 0.2734456605022961 chr6 171115067 12645194 0.07389877596225936 0.28033676491224346 chr7 159138663 10287330 0.06464381317568314 0.2627310170552338 chr8 146364022 10210721 0.06976250625307359 0.27210691010906735 chr9 141213431 7868528 0.055720818793787395 0.24451800944015767 chr10 135534747 7824632 0.05773155720724517 0.24751242367126933 chr11 135006516 8580414 0.06355555460745317 0.2617508559364178 chr12 133851895 8567561 0.06400776768980372 0.26145163319657944 chr13 115169878 7189362 0.062423978603155246 0.2586146681946649 chr14 107349540 5627567 0.05242283292504094 0.2369590602946271 chr15 102531392 4939955 0.04817992717781497 0.2275825830414177 chr16 90354753 3417878 0.037827318281751045 0.20072311335581805 chr17 81195210 3097554 0.03814946719147595 0.2020480896741642 chr18 78077248 5545512 0.07102596648898281 0.27506742524623495 chr19 59128983 1593723 0.0269533301460639 0.1689589277480731 chr20 63025520 2820993 0.04475953550244409 0.21867009364193887 chr21 48129895 2185918 0.045417053164150886 0.22216534323945877 chr22 51304566 1005736 0.0196032454499274 0.14390623892206436 chrMT 16571 336 0.020276386458270474 0.1409441542259392 chrX 155270560 10651405 0.06859899906331245 0.2698809944167671 chrY 59373566 253156 0.0042637829770911856 0.06809527210121977