BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124816.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 22,898,334 number of mapped reads = 22,402,100 (97.83%) number of supplementary alignments = 96,693 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,289,053 number of mapped paired reads (second in pair) = 11,113,047 number of mapped paired reads (both in pair) = 22,138,376 number of mapped paired reads (singletons) = 263,724 number of mapped bases = 1,801,663,020 bp number of sequenced bases = 1,800,700,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,613,421 duplication rate = 6.5% >>>>>>> Insert size mean insert size = 79,656.1473 std insert size = 2,706,149.9338 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.103 >>>>>>> ACTG content number of A's = 515,250,150 bp (28.61%) number of C's = 341,068,353 bp (18.94%) number of T's = 542,067,236 bp (30.1%) number of G's = 402,301,888 bp (22.34%) number of N's = 12,788 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 13,915,160 number of insertions = 280,984 mapped reads with insertion percentage = 1.23% number of deletions = 586,367 mapped reads with deletion percentage = 2.57% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0.582X std coverageData = 6.3382X There is a 25.45% of reference with a coverageData >= 1X There is a 13.08% of reference with a coverageData >= 2X There is a 6.94% of reference with a coverageData >= 3X There is a 3.88% of reference with a coverageData >= 4X There is a 2.24% of reference with a coverageData >= 5X There is a 1.34% of reference with a coverageData >= 6X There is a 0.82% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 145172251 0.582434861817255 7.826189884105049 chr2 243199373 167800677 0.6899716678134692 6.362950716579673 chr3 198022430 129026642 0.6515758947105134 1.6889634369401498 chr4 191154276 81545884 0.426597226629657 4.004232634952313 chr5 180915260 103028304 0.5694837682570282 1.3771764756141844 chr6 171115067 75463407 0.44100971540980666 5.653973218212803 chr7 159138663 169868807 1.0674263802254014 10.005704996624743 chr8 146364022 82545800 0.5639760295737158 2.286224123701607 chr9 141213431 78025172 0.5525336467463919 7.325837502849336 chr10 135534747 89633773 0.6613342702443676 17.05545395486771 chr11 135006516 84475619 0.6257151247425717 4.300788713484227 chr12 133851895 84004746 0.6275947456702051 1.4295466769790661 chr13 115169878 59584242 0.517359599877322 1.2872298233519688 chr14 107349540 51168305 0.47665136711345013 1.692820672585365 chr15 102531392 59286936 0.5782320403881769 1.5049094925470892 chr16 90354753 64358157 0.7122830273245282 11.623713618029443 chr17 81195210 31698024 0.3903927830225453 3.438375274922404 chr18 78077248 51357971 0.6577840832709677 8.233125491202353 chr19 59128983 20688453 0.34988683975843116 4.518785269662257 chr20 63025520 38208991 0.6062463427513173 1.7201457771246724 chr21 48129895 22883155 0.4754457702432137 2.0791872312784845 chr22 51304566 17551909 0.3421120256625892 1.1415609069202384 chrMT 16571 531477 32.07271739786374 21.064885802808597 chrX 155270560 88489297 0.5699038954969957 2.519810954204252 chrY 59373566 5265021 0.08867617956448834 4.832152462110666