BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472656.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 = 14,700,190 number of mapped reads = 14,526,009 (98.82%) number of supplementary alignments = 92,012 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,299,255 number of mapped paired reads (second in pair) = 7,226,754 number of mapped paired reads (both in pair) = 14,405,644 number of mapped paired reads (singletons) = 120,365 number of mapped bases = 1,432,171,181 bp number of sequenced bases = 1,431,949,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,726,599 duplication rate = 47.34% >>>>>>> Insert size mean insert size = 25,836.1372 std insert size = 1,559,720.8276 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 54.7575 >>>>>>> ACTG content number of A's = 394,814,770 bp (27.57%) number of C's = 322,539,478 bp (22.52%) number of T's = 395,780,476 bp (27.64%) number of G's = 318,543,787 bp (22.25%) number of N's = 271,319 bp (0.02%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 9,461,667 number of insertions = 96,944 mapped reads with insertion percentage = 0.66% number of deletions = 83,575 mapped reads with deletion percentage = 0.57% homopolymer indels = 45.54% >>>>>>> Coverage mean coverageData = 0.4626X std coverageData = 21.4034X There is a 3.13% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129051322 0.5177572737120683 23.97330002736986 chr2 243199373 109943343 0.45207083243590435 22.420245518885107 chr3 198022430 181578991 0.9169617350923327 31.387542861919567 chr4 191154276 34144170 0.17862101081118373 11.027090389975806 chr5 180915260 77663146 0.42927913322513533 17.39925478805953 chr6 171115067 115263351 0.6736014134862829 27.415515390072972 chr7 159138663 75620764 0.4751878806472064 15.47733684546039 chr8 146364022 63242189 0.43208835160323755 14.3997026343219 chr9 141213431 107319270 0.7599791977294285 29.15785331868918 chr10 135534747 24457443 0.18045146017057898 9.078487192681637 chr11 135006516 37223250 0.27571446995936105 12.975513288772436 chr12 133851895 55198636 0.41238591355019666 16.73958626366626 chr13 115169878 47461908 0.4121034842113838 22.107610277035207 chr14 107349540 17834714 0.16613684604517168 9.148701891178789 chr15 102531392 19324273 0.1884717706748778 8.576881229864677 chr16 90354753 104052972 1.151604852486288 51.665222740038516 chr17 81195210 48068920 0.5920166965514345 18.152137087544695 chr18 78077248 8461126 0.10836865049341902 4.640526539823391 chr19 59128983 40305624 0.6816559655693722 19.810185878151387 chr20 63025520 53216820 0.8443693919542433 35.32900329331625 chr21 48129895 13065970 0.2714730626360186 22.138452125170627 chr22 51304566 16470758 0.32103883307384373 13.187211791258191 chrMT 16571 6013 0.36286283265946534 0.9449613172442367 chrX 155270560 51523650 0.3318314173659192 9.420041356783713 chrY 59373566 1672558 0.028170078246605567 1.9204145817486633