BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472599.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 = 6,715,172 number of mapped reads = 5,941,836 (88.48%) number of supplementary alignments = 152,712 (2.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,001,320 number of mapped paired reads (second in pair) = 2,940,516 number of mapped paired reads (both in pair) = 5,781,480 number of mapped paired reads (singletons) = 160,356 number of mapped bases = 478,234,511 bp number of sequenced bases = 478,017,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 878,744 duplication rate = 13.09% >>>>>>> Insert size mean insert size = 186,152.5924 std insert size = 4,108,994.0845 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 50.6041 >>>>>>> ACTG content number of A's = 121,908,498 bp (25.5%) number of C's = 95,148,422 bp (19.9%) number of T's = 142,848,046 bp (29.88%) number of G's = 117,824,761 bp (24.65%) number of N's = 288,032 bp (0.06%) GC percentage = 44.55% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 5,711,371 number of insertions = 44,506 mapped reads with insertion percentage = 0.73% number of deletions = 115,786 mapped reads with deletion percentage = 1.91% homopolymer indels = 42.4% >>>>>>> Coverage mean coverageData = 0.1545X std coverageData = 1.5567X There is a 9.14% of reference with a coverageData >= 1X There is a 3.79% of reference with a coverageData >= 2X There is a 1.16% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 26992457 0.10829444232357599 1.5529584858793026 chr2 243199373 38157312 0.15689724660597706 1.8576644807104783 chr3 198022430 23312842 0.11772828966900366 0.49007435105638714 chr4 191154276 23479193 0.12282850005406104 0.7544428184062083 chr5 180915260 21980275 0.12149486450175624 0.5139402889993319 chr6 171115067 26782463 0.1565172691660168 0.7680162776961476 chr7 159138663 44631869 0.28045899191700513 2.414609351173251 chr8 146364022 22791955 0.15572102138597968 1.2882516470731373 chr9 141213431 16097630 0.11399503493403541 1.3668116785914561 chr10 135534747 24083318 0.17769109791454438 1.2947969483128725 chr11 135006516 23547401 0.1744167740762972 1.2461621202415014 chr12 133851895 24182635 0.18066710971854377 0.6296031464956221 chr13 115169878 22073507 0.19166041836043274 0.6546582191548788 chr14 107349540 12367421 0.1152070237096498 5.204289260484629 chr15 102531392 14052074 0.13705143103879835 0.5458116428400294 chr16 90354753 17318375 0.19167087978205197 0.8915147061347795 chr17 81195210 15420408 0.18991770573658223 1.0977601303504245 chr18 78077248 10176777 0.13034241422033727 2.1259493860847845 chr19 59128983 8516843 0.14403838131293414 1.1557947628981955 chr20 63025520 19198020 0.3046070861454217 1.1086049783643042 chr21 48129895 7124968 0.14803622571792438 0.6642073385189633 chr22 51304566 4901189 0.09553124374933802 0.4556879510783456 chrMT 16571 74817 4.514935731096494 4.501724032112284 chrX 155270560 29731151 0.19147964044181975 0.8182320853897812 chrY 59373566 1239611 0.020878163187974932 0.5977410727771867