BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094097.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 714 number of mapped reads = 478 (66.95%) number of supplementary alignments = 39 (5.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 251 number of mapped paired reads (second in pair) = 227 number of mapped paired reads (both in pair) = 394 number of mapped paired reads (singletons) = 84 number of mapped bases = 51,691 bp number of sequenced bases = 50,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60 duplication rate = 8.32% >>>>>>> Insert size mean insert size = 809,491.7973 std insert size = 7,226,691.3284 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 12.4545 >>>>>>> ACTG content number of A's = 16,774 bp (32.97%) number of C's = 10,697 bp (21.02%) number of T's = 12,520 bp (24.6%) number of G's = 10,893 bp (21.41%) number of N's = 0 bp (0%) GC percentage = 42.43% >>>>>>> Mismatches and indels general error rate = 0.0358 number of mismatches = 1,747 number of insertions = 38 mapped reads with insertion percentage = 7.53% number of deletions = 111 mapped reads with deletion percentage = 22.18% homopolymer indels = 24.16% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0068X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 1313 5.267790285665928E-6 0.002404433830972063 chr2 243199373 2301 9.46137307681299E-6 0.00390890716392943 chr3 198022430 3747 1.8922098875364777E-5 0.008746779151111498 chr4 191154276 577 3.018504278711505E-6 0.002039346772567224 chr5 180915260 1151 6.362094607165808E-6 0.0032830612904001895 chr6 171115067 858 5.014169792540829E-6 0.002410172498163773 chr7 159138663 1539 9.67081142311721E-6 0.003701169079076303 chr8 146364022 3689 2.5204281418284612E-5 0.01695285475722971 chr9 141213431 1068 7.563019979310608E-6 0.0032635089688144692 chr10 135534747 1062 7.835629043524906E-6 0.003342231217032389 chr11 135006516 1413 1.046616149993827E-5 0.003710741073285953 chr12 133851895 2058 1.5375202569974823E-5 0.005339371357057689 chr13 115169878 1147 9.959201311301207E-6 0.004374568467694353 chr14 107349540 408 3.8006683587093152E-6 0.002505701625830543 chr15 102531392 894 8.719280822794252E-6 0.0032213713832376888 chr16 90354753 733 8.112467531176804E-6 0.0031752821060612403 chr17 81195210 1071 1.3190433278022189E-5 0.004195162259153352 chr18 78077248 452 5.789138469634585E-6 0.002487196772765452 chr19 59128983 313 5.2935123203455065E-6 0.0023007573316351335 chr20 63025520 399 6.3307688694992125E-6 0.002516093955094828 chr21 48129895 559 1.1614403064872675E-5 0.0042246183739702795 chr22 51304566 628 1.2240625912321331E-5 0.004414894415795331 chrMT 16571 1498 0.09039888962645586 0.5542743786540217 chrX 155270560 21951 1.4137258215594765E-4 0.017935719958657555 chrY 59373566 862 1.4518245375391466E-5 0.005165107655130703