BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617656.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 = 30,599,331 (95.62%) number of supplementary alignments = 165,956 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,471,189 number of mapped paired reads (second in pair) = 15,128,142 number of mapped paired reads (both in pair) = 29,931,930 number of mapped paired reads (singletons) = 667,401 number of mapped bases = 2,966,227,291 bp number of sequenced bases = 2,964,404,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,158,830 duplication rate = 10.95% >>>>>>> Insert size mean insert size = 42,659.0169 std insert size = 1,918,265.9661 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 52.6287 >>>>>>> ACTG content number of A's = 879,593,161 bp (29.67%) number of C's = 591,154,336 bp (19.94%) number of T's = 881,157,648 bp (29.72%) number of G's = 608,902,083 bp (20.54%) number of N's = 3,597,690 bp (0.12%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0147 number of mismatches = 42,703,685 number of insertions = 467,303 mapped reads with insertion percentage = 1.5% number of deletions = 1,094,032 mapped reads with deletion percentage = 3.5% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.9582X std coverageData = 10.5611X There is a 33.48% of reference with a coverageData >= 1X There is a 19.45% of reference with a coverageData >= 2X There is a 11.91% of reference with a coverageData >= 3X There is a 7.63% of reference with a coverageData >= 4X There is a 5.04% of reference with a coverageData >= 5X There is a 3.42% of reference with a coverageData >= 6X There is a 2.38% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.23% of reference with a coverageData >= 9X There is a 0.91% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% 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 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% 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 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 182378563 0.7317075571097574 10.290130585462746 chr2 243199373 306504452 1.2603011603981398 12.185173713792013 chr3 198022430 248073613 1.2527551197104287 2.4998984361125056 chr4 191154276 165166013 0.8640456099449222 8.325398321565283 chr5 180915260 196178927 1.0843691516127496 2.3507397328302293 chr6 171115067 143775817 0.8402288560597647 5.827159727469327 chr7 159138663 232178925 1.458972449705701 13.53802254933722 chr8 146364022 131986394 0.9017680178261295 4.104948712412871 chr9 141213431 121533350 0.8606359121746713 20.12287644696513 chr10 135534747 125595454 0.9266660895452883 21.286467504276267 chr11 135006516 163163277 1.2085585335747795 11.870740854336573 chr12 133851895 126785148 0.9472047295258689 2.18376858119671 chr13 115169878 127228640 1.1047041310576018 2.319107234253099 chr14 107349540 84902801 0.7909004640355236 2.5144100676679404 chr15 102531392 63495359 0.6192772551064166 1.6849222939564368 chr16 90354753 82187244 0.9096062052208809 16.684892849879297 chr17 81195210 73387952 0.9038458303143745 12.788385940675722 chr18 78077248 54534591 0.6984696873537346 18.226470947015198 chr19 59128983 31906526 0.5396089088831445 6.161821475012319 chr20 63025520 80581523 1.2785538778577312 3.072500613135781 chr21 48129895 43288974 0.8994196642232442 4.417242643749784 chr22 51304566 19333209 0.37683213225115286 1.2984365789364056 chrMT 16571 3120041 188.28320560014484 130.15420822662833 chrX 155270560 147084595 0.9472793490279162 4.406531385697086 chrY 59373566 11855903 0.1996831889800926 17.26160886706879