BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238527.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,369,047 number of mapped reads = 2,931,268 (87.01%) number of supplementary alignments = 19,717 (0.59%) number of secondary alignments = 0 number of mapped bases = 180,032,235 bp number of sequenced bases = 179,960,480 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,506,228 duplication rate = 21.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1639 >>>>>>> ACTG content number of A's = 43,233,768 bp (24.02%) number of C's = 31,152,214 bp (17.31%) number of T's = 61,603,766 bp (34.23%) number of G's = 43,966,745 bp (24.43%) number of N's = 3,987 bp (0%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 963,512 number of insertions = 11,409 mapped reads with insertion percentage = 0.39% number of deletions = 42,123 mapped reads with deletion percentage = 1.42% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 1.3099X There is a 0.98% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% 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 0.07% 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 0.05% 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 0.02% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 14651620 0.05878268202990756 1.2509365321310448 chr2 243199373 14191608 0.058353801759184636 2.291815305321336 chr3 198022430 11505235 0.0581006656670156 1.0695120849450122 chr4 191154276 11304823 0.05913978612751514 1.0708372370772719 chr5 180915260 12007855 0.06637281454311814 1.1599093663197642 chr6 171115067 10800148 0.06311628887712149 1.3256597798434255 chr7 159138663 9956086 0.06256233282543036 1.204843599389976 chr8 146364022 9254336 0.06322821601609172 1.1875486783814462 chr9 141213431 7176733 0.05082188676514771 1.0284409820733933 chr10 135534747 8432669 0.062217764718297666 1.1395802440902811 chr11 135006516 7685597 0.05692760044263345 1.0406707395960901 chr12 133851895 8238108 0.06154644280531105 1.1140825664374316 chr13 115169878 6196153 0.05380011777037742 1.158687386450888 chr14 107349540 5546947 0.051671828309650884 1.079677379403843 chr15 102531392 5135431 0.050086426213739495 1.0945805337050716 chr16 90354753 5349102 0.059201113637043536 1.10566856309108 chr17 81195210 4989609 0.061452011762762854 1.103207961841647 chr18 78077248 5290311 0.06775739585493587 2.5317602057439323 chr19 59128983 3488518 0.05899844413018231 1.1483868706180838 chr20 63025520 3683617 0.05844643566606035 1.1181290158530175 chr21 48129895 2416399 0.05020578166646738 0.9830867137245894 chr22 51304566 2234852 0.043560489333444516 0.9017804478148312 chrMT 16571 35664 2.1521935912135657 6.597594925254087 chrX 155270560 9855391 0.06347237364249862 1.1523447939966573 chrY 59373566 605423 0.010196844164623698 0.49420253755111854