BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365340.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 103,631,074 number of mapped reads = 101,178,839 (97.63%) number of supplementary alignments = 834,347 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 50,852,092 number of mapped paired reads (second in pair) = 50,326,747 number of mapped paired reads (both in pair) = 100,472,974 number of mapped paired reads (singletons) = 705,865 number of mapped bases = 13,250,771,718 bp number of sequenced bases = 13,245,612,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,882,016 duplication rate = 30% >>>>>>> Insert size mean insert size = 84,714.5664 std insert size = 2,843,086.9608 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 54.1468 >>>>>>> ACTG content number of A's = 3,955,033,383 bp (29.86%) number of C's = 2,625,235,119 bp (19.82%) number of T's = 3,900,726,923 bp (29.45%) number of G's = 2,764,142,365 bp (20.87%) number of N's = 474,465 bp (0%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 100,033,711 number of insertions = 3,944,014 mapped reads with insertion percentage = 3.78% number of deletions = 2,096,432 mapped reads with deletion percentage = 2% homopolymer indels = 49.6% >>>>>>> Coverage mean coverageData = 4.2804X std coverageData = 49.7979X There is a 67.87% of reference with a coverageData >= 1X There is a 59.68% of reference with a coverageData >= 2X There is a 49.45% of reference with a coverageData >= 3X There is a 42.18% of reference with a coverageData >= 4X There is a 34.65% of reference with a coverageData >= 5X There is a 28.99% of reference with a coverageData >= 6X There is a 23.61% of reference with a coverageData >= 7X There is a 19.51% of reference with a coverageData >= 8X There is a 15.79% of reference with a coverageData >= 9X There is a 12.93% of reference with a coverageData >= 10X There is a 10.43% of reference with a coverageData >= 11X There is a 8.48% of reference with a coverageData >= 12X There is a 6.82% of reference with a coverageData >= 13X There is a 5.53% of reference with a coverageData >= 14X There is a 4.43% of reference with a coverageData >= 15X There is a 3.59% of reference with a coverageData >= 16X There is a 2.88% of reference with a coverageData >= 17X There is a 2.33% of reference with a coverageData >= 18X There is a 1.88% of reference with a coverageData >= 19X There is a 1.52% of reference with a coverageData >= 20X There is a 1.23% of reference with a coverageData >= 21X There is a 1.01% of reference with a coverageData >= 22X There is a 0.82% of reference with a coverageData >= 23X There is a 0.68% of reference with a coverageData >= 24X There is a 0.56% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.39% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.28% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1083707013 4.347860834416938 132.7009358094025 chr2 243199373 1142174852 4.6964547560737335 28.723043506557012 chr3 198022430 891219015 4.500596296086257 6.8795389948599155 chr4 191154276 899538971 4.705827093295051 25.123074123680492 chr5 180915260 812647336 4.491867275319948 6.149460654601424 chr6 171115067 783327916 4.577784585152867 21.51585821485621 chr7 159138663 891513493 5.602117525644915 34.007212624735615 chr8 146364022 671206343 4.585869763813951 15.986303533191672 chr9 141213431 555201945 3.9316511260178926 44.644057584150474 chr10 135534747 684663344 5.051570605728139 101.02043922028865 chr11 135006516 602137547 4.460062853558861 32.6548994349879 chr12 133851895 592861918 4.429238136673373 22.020831726920502 chr13 115169878 435521264 3.7815553125792145 4.902113893541257 chr14 107349540 398469709 3.7118902325990404 5.364169039745897 chr15 102531392 363229525 3.54261770873061 11.479583844408603 chr16 90354753 374487855 4.144639242165821 16.737046673932404 chr17 81195210 353916726 4.358837497926294 26.93265576676726 chr18 78077248 366406469 4.692871206218744 48.655434256779856 chr19 59128983 242264323 4.097217822941416 68.10660498666905 chr20 63025520 262414395 4.163621260086391 10.038584394745536 chr21 48129895 187356638 3.892728999304902 17.64323019487457 chr22 51304566 154036970 3.0024027491042413 15.32670952120655 chrMT 16571 25693874 1550.5324965300827 320.7286087350653 chrX 155270560 357074075 2.2996894903966343 11.183502991085229 chrY 59373566 119700202 2.016052092946548 44.48776201547941