BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053602.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,879,714 number of mapped reads = 5,443,734 (61.31%) number of supplementary alignments = 184 (0%) number of secondary alignments = 0 number of mapped bases = 254,242,401 bp number of sequenced bases = 254,188,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,185,219 duplication rate = 15.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4906 >>>>>>> ACTG content number of A's = 76,938,460 bp (30.27%) number of C's = 48,666,611 bp (19.15%) number of T's = 76,356,485 bp (30.04%) number of G's = 52,115,630 bp (20.5%) number of N's = 111,403 bp (0.04%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,403,083 number of insertions = 14,138 mapped reads with insertion percentage = 0.26% number of deletions = 38,203 mapped reads with deletion percentage = 0.7% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.0821X std coverageData = 0.8636X There is a 3.97% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% 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 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 19813580 0.07949260034140497 0.6886162224570018 chr2 243199373 21955528 0.09027789722138799 2.114080928307398 chr3 198022430 17797532 0.08987634380610318 0.6569534327486899 chr4 191154276 16918710 0.08850814302474719 0.6769491178495267 chr5 180915260 16037974 0.08864909460926623 0.6426193018430079 chr6 171115067 15072510 0.08808406100206242 0.6950300436279454 chr7 159138663 13715424 0.0861853665315763 0.7525339421291375 chr8 146364022 12920141 0.0882740226966433 0.6827210393484585 chr9 141213431 10443714 0.07395694535599805 0.6106563500312554 chr10 135534747 11605084 0.08562441924947851 0.6728390109587331 chr11 135006516 11494571 0.08514086090481736 0.6854190400834114 chr12 133851895 11590065 0.08658872554624647 0.6359630521039471 chr13 115169878 8438314 0.0732684113809689 0.590270487194773 chr14 107349540 7758001 0.07226860031258635 0.6321322529802034 chr15 102531392 7347896 0.07166484192470536 0.5804384154286647 chr16 90354753 6950583 0.07692548282435126 0.6178211667199356 chr17 81195210 6373634 0.07849766014522286 0.5954001651896579 chr18 78077248 6707457 0.08590795874362785 0.7098063184200102 chr19 59128983 4448197 0.07522870806014031 0.6486925786627283 chr20 63025520 5248017 0.08326812694286378 0.6327252983399346 chr21 48129895 3250449 0.06753492813562133 0.6071325440062139 chr22 51304566 2620839 0.051083932763411354 0.4526615842907616 chrMT 16571 17265 1.0418803934584515 3.057393771724586 chrX 155270560 15078422 0.0971106306308163 0.7248707792583057 chrY 59373566 638494 0.010753842880180045 0.21527767969942935