BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038400.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 16,201,984 number of mapped reads = 15,508,628 (95.72%) number of supplementary alignments = 249,817 (1.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,824,852 number of mapped paired reads (second in pair) = 7,683,776 number of mapped paired reads (both in pair) = 15,345,466 number of mapped paired reads (singletons) = 163,162 number of mapped bases = 2,238,935,354 bp number of sequenced bases = 2,237,387,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,397,184 duplication rate = 10.21% >>>>>>> Insert size mean insert size = 80,778.142 std insert size = 2,706,179.6784 median insert size = 250 >>>>>>> Mapping quality mean mapping quality = 53.9102 >>>>>>> ACTG content number of A's = 657,462,764 bp (29.39%) number of C's = 456,246,594 bp (20.39%) number of T's = 656,167,316 bp (29.33%) number of G's = 467,462,012 bp (20.89%) number of N's = 48,816 bp (0%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 30,407,361 number of insertions = 397,594 mapped reads with insertion percentage = 2.42% number of deletions = 814,029 mapped reads with deletion percentage = 5.04% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.7232X std coverageData = 10.2367X There is a 26.97% of reference with a coverageData >= 1X There is a 15.82% of reference with a coverageData >= 2X There is a 8.99% of reference with a coverageData >= 3X There is a 5.64% of reference with a coverageData >= 4X There is a 3.47% of reference with a coverageData >= 5X There is a 2.23% of reference with a coverageData >= 6X There is a 1.43% of reference with a coverageData >= 7X There is a 0.94% of reference with a coverageData >= 8X There is a 0.63% of reference with a coverageData >= 9X There is a 0.43% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 175388772 0.7036643330970879 12.21208088699679 chr2 243199373 210714011 0.8664249763505764 14.112788826645788 chr3 198022430 154764990 0.7815528271216549 1.718682914270811 chr4 191154276 152048214 0.7954214636558797 6.71784416752666 chr5 180915260 139103180 0.7688858308580492 1.8430132463412536 chr6 171115067 139391243 0.8146053146798581 14.340154094733588 chr7 159138663 120179811 0.7551892716353913 10.263182690186266 chr8 146364022 116648708 0.7969766504503408 3.394317233445302 chr9 141213431 98586844 0.6981407030610283 22.18385614833566 chr10 135534747 118648775 0.875412229160689 17.1043747410646 chr11 135006516 104631439 0.7750102891330075 6.991954097087071 chr12 133851895 97446775 0.7280193903866659 1.7004931107842416 chr13 115169878 72123348 0.626234474260709 1.5058527023305848 chr14 107349540 66427937 0.6188003879662642 1.6859605374736268 chr15 102531392 60955223 0.5945030279116859 1.4808183869935743 chr16 90354753 73186542 0.8099910582457128 12.560035046707757 chr17 81195210 50773520 0.6253265432776145 8.229782638479287 chr18 78077248 67137444 0.8598848668436675 18.40222279228552 chr19 59128983 27698813 0.46844730950302327 6.659044677170736 chr20 63025520 45032206 0.7145074883951771 2.481259755130731 chr21 48129895 29458787 0.6120683828626677 3.463361554591628 chr22 51304566 19489660 0.37988158792728116 1.2717623327000391 chrMT 16571 2893005 174.58240299318086 110.34198812298114 chrX 155270560 69290864 0.44625886581461416 2.27374408701014 chrY 59373566 26915243 0.4533203041905888 10.845370989755736