BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971319.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 75,490,972 number of mapped reads = 65,369,404 (86.59%) number of secondary alignments = 0 number of mapped bases = 2,590,810,690 bp number of sequenced bases = 2,590,482,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,165,595 duplication rate = 14.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1567 >>>>>>> ACTG content number of A's = 783,372,867 bp (30.24%) number of C's = 501,426,485 bp (19.36%) number of T's = 796,021,937 bp (30.73%) number of G's = 509,412,587 bp (19.66%) number of N's = 248,795 bp (0.01%) GC percentage = 39.02% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 7,113,816 number of insertions = 84,363 mapped reads with insertion percentage = 0.13% number of deletions = 258,127 mapped reads with deletion percentage = 0.39% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 0.8369X std coverageData = 4.7398X There is a 27.19% of reference with a coverageData >= 1X There is a 17.15% of reference with a coverageData >= 2X There is a 11.35% of reference with a coverageData >= 3X There is a 7.69% of reference with a coverageData >= 4X There is a 5.29% of reference with a coverageData >= 5X There is a 3.67% of reference with a coverageData >= 6X There is a 2.58% of reference with a coverageData >= 7X There is a 1.84% of reference with a coverageData >= 8X There is a 1.33% of reference with a coverageData >= 9X There is a 0.98% of reference with a coverageData >= 10X There is a 0.73% of reference with a coverageData >= 11X There is a 0.55% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% 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 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 209122217 0.8390037953004739 9.382383378492062 chr2 243199373 230551384 0.9479933322032044 4.021887854975593 chr3 198022430 176522814 0.8914283801082534 2.2085441360042988 chr4 191154276 184432678 0.9648367897352189 2.432430666192265 chr5 180915260 170870706 0.9444792329845476 2.3411453385806595 chr6 171115067 154661297 0.9038438269144353 3.2461659300779173 chr7 159138663 143256503 0.9001992369384176 7.801040724322911 chr8 146364022 139666486 0.9542405578332631 8.295748010594838 chr9 141213431 113710806 0.8052407281287571 3.6345953395020754 chr10 135534747 122419002 0.9032296492942876 3.4102162271211753 chr11 135006516 115455671 0.8551859156190654 3.8970504300344335 chr12 133851895 122175407 0.9127656130680855 2.417412320781415 chr13 115169878 80620001 0.7000094330220615 1.904965486007627 chr14 107349540 81509953 0.7592948511935869 2.9312570686973474 chr15 102531392 75867757 0.7399466204457655 1.9628750332087035 chr16 90354753 68228168 0.7551143214347562 2.3624483114622907 chr17 81195210 64164553 0.7902504716719126 2.4436055142251236 chr18 78077248 69221510 0.8865772266973344 7.1957169252593705 chr19 59128983 45166015 0.7638557727265494 7.652054199757215 chr20 63025520 51222113 0.8127201965172203 2.2365122776993807 chr21 48129895 34736562 0.721725281137638 2.5723816158740105 chr22 51304566 25819468 0.5032586768203049 2.195182242973447 chrMT 16571 28209 1.7023112666706897 2.1806771574505124 chrX 155270560 90140960 0.5805412178586848 2.6647359854111987 chrY 59373566 21240450 0.35774253478391377 2.8657982078757245