BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472737.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 = 18,990,156 number of mapped reads = 18,776,229 (98.87%) number of supplementary alignments = 65,225 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,431,074 number of mapped paired reads (second in pair) = 9,345,155 number of mapped paired reads (both in pair) = 18,648,714 number of mapped paired reads (singletons) = 127,515 number of mapped bases = 1,851,872,000 bp number of sequenced bases = 1,851,606,117 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,802,592 duplication rate = 47.43% >>>>>>> Insert size mean insert size = 21,715.5519 std insert size = 1,442,669.6334 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 55.1916 >>>>>>> ACTG content number of A's = 512,282,214 bp (27.67%) number of C's = 416,139,000 bp (22.47%) number of T's = 508,901,890 bp (27.48%) number of G's = 413,931,801 bp (22.36%) number of N's = 351,212 bp (0.02%) GC percentage = 44.83% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 12,402,563 number of insertions = 112,535 mapped reads with insertion percentage = 0.59% number of deletions = 102,051 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 0.5982X std coverageData = 18.8701X There is a 5.45% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 195040499 0.7825075749761121 23.86549349456955 chr2 243199373 119649918 0.4919828391169413 14.038383073457455 chr3 198022430 222103605 1.1216083198251834 26.584648325562323 chr4 191154276 83702742 0.4378805630275307 19.709888928050777 chr5 180915260 97153784 0.5370126544327991 14.676561946642574 chr6 171115067 108478646 0.6339514567703147 15.455762693353696 chr7 159138663 80134658 0.5035524145380058 14.676281087549064 chr8 146364022 97014556 0.6628306237717354 24.880316496786357 chr9 141213431 94265230 0.6675372826257582 15.79756532185319 chr10 135534747 55229048 0.407489955324888 16.222796890664256 chr11 135006516 91219381 0.6756665063484788 26.598421220952638 chr12 133851895 76884719 0.5744014233044665 16.501290245793044 chr13 115169878 46237876 0.4014754274550851 17.363374302459192 chr14 107349540 43193147 0.40235987038230436 12.022909522466144 chr15 102531392 54171741 0.5283429781193256 18.85654683288191 chr16 90354753 80915759 0.895534062275617 21.962989926615826 chr17 81195210 74604441 0.9188281057466321 20.74424095629614 chr18 78077248 34170008 0.43764360137283526 16.47873182195979 chr19 59128983 39165132 0.6623677596484282 17.069795008051425 chr20 63025520 34860713 0.5531205930550037 17.338190045215207 chr21 48129895 8803483 0.18291091223033001 7.466443242746214 chr22 51304566 16380794 0.3192853049375761 10.460399882446763 chrMT 16571 4959 0.29925773942429545 0.8964415597340025 chrX 155270560 95535022 0.6152809779265304 19.566157173199354 chrY 59373566 2952139 0.04972143664067609 1.5515877006643042