BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536743.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 19,268,535 number of mapped reads = 15,658,881 (81.27%) number of supplementary alignments = 349 (0%) number of secondary alignments = 0 number of mapped bases = 780,522,876 bp number of sequenced bases = 780,456,389 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 150,744 duplication rate = 0.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4448 >>>>>>> ACTG content number of A's = 245,507,038 bp (31.46%) number of C's = 144,038,316 bp (18.46%) number of T's = 244,779,617 bp (31.36%) number of G's = 146,114,553 bp (18.72%) number of N's = 16,865 bp (0%) GC percentage = 37.18% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 2,683,780 number of insertions = 56,745 mapped reads with insertion percentage = 0.36% number of deletions = 40,075 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.32% >>>>>>> Coverage mean coverageData = 0.2521X std coverageData = 3.3143X There is a 20.17% of reference with a coverageData >= 1X There is a 4.05% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.02% 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 58037708 0.23284880000359157 0.5475336379657344 chr2 243199373 73287906 0.3013490746129514 0.6044474857701696 chr3 198022430 64649720 0.3264767531637704 0.6332789337652356 chr4 191154276 69258993 0.36231987298050294 0.667796242667127 chr5 180915260 57796023 0.31946461011636057 0.6797336435372946 chr6 171115067 55296731 0.32315524266486717 13.904571825061089 chr7 159138663 45170952 0.283846496812657 0.5939273257836526 chr8 146364022 43759126 0.29897460729796016 0.5957341239892231 chr9 141213431 32199658 0.22802121421439014 0.5363012012967578 chr10 135534747 32397620 0.2390355293908506 0.534229209334236 chr11 135006516 35137928 0.2602683858607239 0.56375673246093 chr12 133851895 35374224 0.2642788434186905 0.5685748286019744 chr13 115169878 35998902 0.31257219878274073 0.626037044256705 chr14 107349540 24121986 0.22470507092997324 0.5312673658229318 chr15 102531392 19027444 0.18557676462638875 0.478932603964844 chr16 90354753 12400965 0.1372475114839836 0.40839049822320683 chr17 81195210 9702320 0.11949374846127006 0.38099582087797773 chr18 78077248 25293841 0.3239591769423021 0.6239914443852312 chr19 59128983 3443815 0.05824241895044939 0.25734030229545685 chr20 63025520 11533399 0.18299569761582293 0.4752894177927397 chr21 48129895 10541830 0.21902873463571862 0.5399332297420859 chr22 51304566 2885941 0.05625115316246901 0.25451859614648265 chrMT 16571 2430 0.14664172349284896 0.3762341638301497 chrX 155270560 20171982 0.12991504635521375 0.3760694717560687 chrY 59373566 3031432 0.0510569299475797 0.24490795507297958