BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617362.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,068,514 (93.96%) number of supplementary alignments = 67,268 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,121,612 number of mapped paired reads (second in pair) = 14,946,902 number of mapped paired reads (both in pair) = 29,490,214 number of mapped paired reads (singletons) = 578,300 number of mapped bases = 2,949,308,839 bp number of sequenced bases = 2,948,434,212 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,536,301 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 54,111.3497 std insert size = 2,220,048.4355 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.437 >>>>>>> ACTG content number of A's = 891,879,852 bp (30.25%) number of C's = 585,798,140 bp (19.87%) number of T's = 879,050,832 bp (29.81%) number of G's = 589,764,049 bp (20%) number of N's = 1,941,339 bp (0.07%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0123 number of mismatches = 35,529,071 number of insertions = 301,814 mapped reads with insertion percentage = 0.97% number of deletions = 362,532 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.07% >>>>>>> Coverage mean coverageData = 0.9527X std coverageData = 9.5962X There is a 52.95% of reference with a coverageData >= 1X There is a 23.83% of reference with a coverageData >= 2X There is a 9.12% of reference with a coverageData >= 3X There is a 3.19% of reference with a coverageData >= 4X There is a 1.09% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% 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 0.02% 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 0.01% 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 192020442 0.7703910274309808 19.604107932156587 chr2 243199373 290721399 1.1954035712090425 8.61848119721204 chr3 198022430 234544672 1.1844348743725648 1.4629825607200284 chr4 191154276 161535133 0.8450511093981492 9.235455093433458 chr5 180915260 185233721 1.0238700759681632 1.4327842987370702 chr6 171115067 137902356 0.8059042281764702 3.6138451572415233 chr7 159138663 239528017 1.505152880415993 10.691863645804894 chr8 146364022 124025685 0.8473782238643319 7.510341107890266 chr9 141213431 124158403 0.879225170869193 14.34997321785349 chr10 135534747 124046764 0.9152395732143876 19.78855881613168 chr11 135006516 158177409 1.1716279605348827 5.381041071406583 chr12 133851895 130144501 0.9723022673679741 1.3661657421512192 chr13 115169878 128422497 1.1150701835422627 1.2877839730702747 chr14 107349540 85562030 0.7970414218821991 1.3637635082125628 chr15 102531392 66201683 0.6456723322355752 0.9722119815876599 chr16 90354753 74182725 0.8210163000500925 7.810008688123248 chr17 81195210 91858112 1.131324273931923 6.939996651562088 chr18 78077248 53057965 0.6795573148274898 14.976947650877676 chr19 59128983 54970894 0.9296776506370826 9.413291491950742 chr20 63025520 84807690 1.3456087311933325 2.392734044972383 chr21 48129895 46896127 0.9743658696949162 3.114353142340666 chr22 51304566 26418760 0.5149397424003158 0.9142186824172189 chrMT 16571 2028363 122.4043811477883 20.179145121528183 chrX 155270560 122947582 0.7918280323069615 2.9306114489048154 chrY 59373566 9915909 0.1670088166845158 8.020761004138075