BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617500.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 = 30,490,417 (95.28%) number of supplementary alignments = 158,233 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,351,919 number of mapped paired reads (second in pair) = 15,138,498 number of mapped paired reads (both in pair) = 29,944,362 number of mapped paired reads (singletons) = 546,055 number of mapped bases = 2,971,849,985 bp number of sequenced bases = 2,970,086,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,280,109 duplication rate = 9.95% >>>>>>> Insert size mean insert size = 40,432.4223 std insert size = 1,883,357.0029 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.7205 >>>>>>> ACTG content number of A's = 876,174,711 bp (29.5%) number of C's = 600,499,530 bp (20.22%) number of T's = 875,810,450 bp (29.49%) number of G's = 614,924,216 bp (20.7%) number of N's = 2,677,247 bp (0.09%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 36,727,182 number of insertions = 441,859 mapped reads with insertion percentage = 1.42% number of deletions = 1,034,945 mapped reads with deletion percentage = 3.32% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.96X std coverageData = 9.6506X There is a 38.21% of reference with a coverageData >= 1X There is a 20.62% of reference with a coverageData >= 2X There is a 11.65% of reference with a coverageData >= 3X There is a 6.93% of reference with a coverageData >= 4X There is a 4.27% of reference with a coverageData >= 5X There is a 2.74% of reference with a coverageData >= 6X There is a 1.81% of reference with a coverageData >= 7X There is a 1.24% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% 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 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% 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 191569432 0.7685815635339982 9.380529453480303 chr2 243199373 307164506 1.2630152052242338 11.339559897109725 chr3 198022430 245319993 1.2388495232585521 2.252740383774535 chr4 191154276 153579965 0.8034346299425705 6.101886911074432 chr5 180915260 190430848 1.052596934056309 2.0867248643667478 chr6 171115067 140152601 0.8190547066203118 5.438661643252199 chr7 159138663 229047809 1.4392970550468933 13.194056717274865 chr8 146364022 132083894 0.9024341651392991 3.836859385620948 chr9 141213431 123361246 0.8735801200099728 18.180135038672947 chr10 135534747 125718233 0.9275719753252647 18.622324844508427 chr11 135006516 167279724 1.2390492618889595 12.502766192697024 chr12 133851895 129899954 0.9704752704472357 2.0146029123878146 chr13 115169878 125958069 1.0936719842665805 2.1319867717368512 chr14 107349540 86657202 0.8072433472933372 2.230307779770688 chr15 102531392 66985792 0.6533198339880141 1.5210144337515548 chr16 90354753 79967401 0.8850381230083159 14.854710257703086 chr17 81195210 83085151 1.0232765085526596 13.549409774047218 chr18 78077248 53274744 0.6823337830759608 16.9778310068143 chr19 59128983 35657086 0.6030390544684322 5.788453702548957 chr20 63025520 87757677 1.3924149614314962 2.803051328691643 chr21 48129895 42785138 0.8889514095137752 3.8052290854040787 chr22 51304566 22245343 0.4335938247679553 1.2529635627366795 chrMT 16571 2087333 125.9630076639913 95.62698504352707 chrX 155270560 139551467 0.8987632104888396 4.072569946852642 chrY 59373566 10229377 0.17228840524754738 13.534590639208831