BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234115.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,560,353 number of mapped reads = 1,019,411 (65.33%) number of supplementary alignments = 4,006 (0.26%) number of secondary alignments = 0 number of mapped bases = 62,059,987 bp number of sequenced bases = 62,015,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,664 duplication rate = 4.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8743 >>>>>>> ACTG content number of A's = 15,989,742 bp (25.78%) number of C's = 10,651,349 bp (17.18%) number of T's = 19,934,596 bp (32.14%) number of G's = 15,425,864 bp (24.87%) number of N's = 14,013 bp (0.02%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 580,449 number of insertions = 5,219 mapped reads with insertion percentage = 0.51% number of deletions = 24,712 mapped reads with deletion percentage = 2.39% homopolymer indels = 46.17% >>>>>>> Coverage mean coverageData = 0.02X std coverageData = 0.2083X There is a 1.7% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% 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 5364109 0.021520945378105998 0.27926419838695726 chr2 243199373 4580980 0.018836315009743056 0.23678728237540278 chr3 198022430 4966957 0.025082799963620284 0.18430986176199204 chr4 191154276 3131732 0.016383269396495218 0.15608249458440362 chr5 180915260 3656645 0.020211921316090196 0.16619038299036196 chr6 171115067 3873044 0.022634149452192893 0.1995486650948961 chr7 159138663 3786317 0.023792565104056453 0.304675034070137 chr8 146364022 3032139 0.02071642305648037 0.24596006411455862 chr9 141213431 2496241 0.01767707917244784 0.1964923901919458 chr10 135534747 3036928 0.022407006817225992 0.19650003073177208 chr11 135006516 2920320 0.02163095594585968 0.22197921928633588 chr12 133851895 2473575 0.018479940086018207 0.15879778407735298 chr13 115169878 2237610 0.0194287780699047 0.17329951673084498 chr14 107349540 2492897 0.02322224203289553 0.1837294626987958 chr15 102531392 1494709 0.014578062102190127 0.14624578035989558 chr16 90354753 1735298 0.01920538701489229 0.16843641155910435 chr17 81195210 1770029 0.02179967266541955 0.1862797028490383 chr18 78077248 1456193 0.018650670167063264 0.287697128391891 chr19 59128983 1629569 0.02755956414809299 0.23732575149133991 chr20 63025520 1459356 0.023155001339140082 0.18585693493413086 chr21 48129895 947593 0.019688241580414833 0.16435019112129223 chr22 51304566 638314 0.012441660650632928 0.12898021541360952 chrMT 16571 41332 2.494236919920343 2.8359486547292345 chrX 155270560 2598188 0.016733294450667274 0.16414752308853375 chrY 59373566 239912 0.004040720747680878 0.08323079986746344