BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231736.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 = 1,468,513 number of mapped reads = 679,897 (46.3%) number of supplementary alignments = 4,680 (0.32%) number of secondary alignments = 0 number of mapped bases = 43,439,927 bp number of sequenced bases = 43,414,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,193 duplication rate = 9.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.68 >>>>>>> ACTG content number of A's = 12,103,808 bp (27.88%) number of C's = 7,339,518 bp (16.91%) number of T's = 14,546,191 bp (33.51%) number of G's = 9,423,998 bp (21.71%) number of N's = 1,243 bp (0%) GC percentage = 38.61% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 413,061 number of insertions = 4,366 mapped reads with insertion percentage = 0.63% number of deletions = 14,446 mapped reads with deletion percentage = 2.1% homopolymer indels = 45.9% >>>>>>> Coverage mean coverageData = 0.014X std coverageData = 0.3359X There is a 0.87% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 2481937 0.009957596053491878 0.27160828976258566 chr2 243199373 2765918 0.011373047413243126 0.2009534384477714 chr3 198022430 2989821 0.015098395671641843 0.18731453680038582 chr4 191154276 3300089 0.017264008261055064 0.2116200408169066 chr5 180915260 4175956 0.023082386748359426 0.2379978039098813 chr6 171115067 1916399 0.011199475496801226 0.1672645047022042 chr7 159138663 1786888 0.011228496999500367 0.18267678567431053 chr8 146364022 1736661 0.011865354451656158 1.220628278991542 chr9 141213431 1487318 0.010532411750550839 0.212921879123749 chr10 135534747 3087957 0.022783508054949185 0.2419723203724677 chr11 135006516 3205899 0.023746253847480962 0.2718310423705318 chr12 133851895 1318214 0.009848302857423124 0.1515989288114284 chr13 115169878 2457714 0.021339902782566113 0.23426714155409076 chr14 107349540 1680377 0.01565332278088942 0.19479033116855995 chr15 102531392 844844 0.00823985692108813 0.1366123873164177 chr16 90354753 958185 0.01060469945615368 0.15862168225320195 chr17 81195210 1424578 0.017545099027393363 0.20709771836856056 chr18 78077248 835449 0.010700287489641028 0.3232012499541223 chr19 59128983 703344 0.01189508028575428 0.21152416908145372 chr20 63025520 750347 0.011905447190281016 0.16535298496625023 chr21 48129895 808982 0.016808305939582872 0.21452458149136652 chr22 51304566 433263 0.008444920867277193 0.1287642954988353 chrMT 16571 35998 2.172349284895299 2.7375913069087443 chrX 155270560 2019807 0.013008306275188291 0.18028006293029467 chrY 59373566 233982 0.0039408446513049256 0.11367445623315889