BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472750.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,963,470 number of mapped reads = 12,807,986 (98.8%) number of supplementary alignments = 41,422 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,431,535 number of mapped paired reads (second in pair) = 6,376,451 number of mapped paired reads (both in pair) = 12,725,288 number of mapped paired reads (singletons) = 82,698 number of mapped bases = 1,262,926,714 bp number of sequenced bases = 1,262,746,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,902,756 duplication rate = 47.03% >>>>>>> Insert size mean insert size = 22,833.2988 std insert size = 1,453,204.8638 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 55.1118 >>>>>>> ACTG content number of A's = 351,553,456 bp (27.84%) number of C's = 281,824,333 bp (22.32%) number of T's = 349,689,357 bp (27.69%) number of G's = 279,437,647 bp (22.13%) number of N's = 241,984 bp (0.02%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 8,315,511 number of insertions = 80,643 mapped reads with insertion percentage = 0.62% number of deletions = 71,451 mapped reads with deletion percentage = 0.55% homopolymer indels = 44.88% >>>>>>> Coverage mean coverageData = 0.408X std coverageData = 15.1022X There is a 3.42% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 116579741 0.4677209650763518 18.392998165090646 chr2 243199373 75172809 0.3090995181143004 11.420062533958456 chr3 198022430 156957689 0.7926258101165611 17.760820475038557 chr4 191154276 38690189 0.20240294807739484 7.096357001003634 chr5 180915260 68854144 0.38058781774406425 12.641807693353417 chr6 171115067 65525624 0.382933105475744 12.155062959084184 chr7 159138663 60337325 0.3791493774206209 13.972568049112596 chr8 146364022 75149968 0.513445633517778 17.608334404752668 chr9 141213431 79053887 0.5598184708082052 20.24623047890304 chr10 135534747 35573530 0.2624679706673301 12.33502939703434 chr11 135006516 51376839 0.3805508098586886 12.271391711500746 chr12 133851895 56563871 0.4225855076612849 13.820893976570522 chr13 115169878 36073239 0.31321765401192836 13.903421670247937 chr14 107349540 24882378 0.2317883989069725 12.258064833823768 chr15 102531392 32766817 0.3195783882462066 10.426194662964063 chr16 90354753 48780189 0.539874078345386 13.788615966761714 chr17 81195210 37059433 0.4564238826403676 14.887727852752851 chr18 78077248 21286825 0.2726380033271664 15.025258541832804 chr19 59128983 24299764 0.41096198119964283 12.339017383345155 chr20 63025520 22593309 0.3584787400405423 10.081172254620757 chr21 48129895 4703714 0.09772957119478445 3.5963084023882184 chr22 51304566 20125598 0.3922769369104496 15.391436936400542 chrMT 16571 3799 0.2292559290326474 0.7000114969962414 chrX 155270560 104684609 0.6742077120092824 28.95395503922248 chrY 59373566 5831424 0.09821582890945105 5.94639747245501