BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472531.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 = 16,502,702 number of mapped reads = 16,314,280 (98.86%) number of supplementary alignments = 63,476 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,183,951 number of mapped paired reads (second in pair) = 8,130,329 number of mapped paired reads (both in pair) = 16,213,328 number of mapped paired reads (singletons) = 100,952 number of mapped bases = 1,607,316,962 bp number of sequenced bases = 1,607,114,714 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,148,920 duplication rate = 45.51% >>>>>>> Insert size mean insert size = 30,913.7377 std insert size = 1,788,262.6973 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 54.999 >>>>>>> ACTG content number of A's = 439,519,657 bp (27.35%) number of C's = 366,546,551 bp (22.81%) number of T's = 436,719,168 bp (27.17%) number of G's = 364,079,191 bp (22.65%) number of N's = 250,147 bp (0.02%) GC percentage = 45.46% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 9,934,128 number of insertions = 97,572 mapped reads with insertion percentage = 0.59% number of deletions = 79,679 mapped reads with deletion percentage = 0.48% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.5192X std coverageData = 17.9491X There is a 5.16% of reference with a coverageData >= 1X There is a 2.22% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 165964140 0.6658524634127191 24.881368275849688 chr2 243199373 123286667 0.5069366153341193 20.59583258158588 chr3 198022430 149753692 0.7562461080797767 19.097938375187155 chr4 191154276 72131102 0.37734495669874524 13.75469778438888 chr5 180915260 98318942 0.5434530066728478 19.372194447077177 chr6 171115067 89982537 0.5258598122163024 15.221197375454794 chr7 159138663 80982191 0.5088781662065365 18.356714988400196 chr8 146364022 72622895 0.4961799628599985 16.38915595136173 chr9 141213431 80640399 0.5710533228245124 14.43080666478425 chr10 135534747 50251181 0.3707623477542626 14.1823155557364 chr11 135006516 70331929 0.5209521072301428 16.716067509350378 chr12 133851895 76830102 0.5739933827608492 15.691777012654518 chr13 115169878 45528415 0.3953153011067703 16.69546771236357 chr14 107349540 48567114 0.452420327092226 19.396901320673045 chr15 102531392 39892005 0.3890711344287611 11.093742405608388 chr16 90354753 68471693 0.7578095310603085 26.532581771703246 chr17 81195210 82038244 1.0103828046014045 26.395941574093815 chr18 78077248 31096512 0.39827879179348125 13.70844983918965 chr19 59128983 18867912 0.31909752278337006 7.131249873008514 chr20 63025520 29912217 0.47460484260978725 12.813593599014899 chr21 48129895 4542680 0.0943837504735882 3.048135025226736 chr22 51304566 13906234 0.27105256089682156 7.584743778332214 chrMT 16571 2037 0.12292559290326474 0.4822978565702307 chrX 155270560 90520040 0.5829826336686105 20.72080072850296 chrY 59373566 2876082 0.048440445702722316 1.7791552736059102