BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013234.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 = 1,887,655 number of mapped reads = 1,691,189 (89.59%) number of supplementary alignments = 14,683 (0.78%) number of secondary alignments = 0 number of mapped bases = 114,616,609 bp number of sequenced bases = 114,571,450 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,449 duplication rate = 4.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2216 >>>>>>> ACTG content number of A's = 32,335,011 bp (28.22%) number of C's = 20,954,501 bp (18.29%) number of T's = 36,758,231 bp (32.08%) number of G's = 24,498,836 bp (21.38%) number of N's = 24,871 bp (0.02%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 902,697 number of insertions = 8,708 mapped reads with insertion percentage = 0.51% number of deletions = 25,752 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.3929X There is a 2.96% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9040024 0.03626881234530605 0.7383884854621268 chr2 243199373 9773933 0.0401889728556167 0.42489492663296985 chr3 198022430 7932194 0.04005704808288637 0.23870872986050495 chr4 191154276 7777851 0.04068886745698537 0.2641254989380087 chr5 180915260 7046476 0.03894904166735299 0.23787529186283984 chr6 171115067 6798821 0.03973245091269491 0.27917134470199606 chr7 159138663 6428041 0.04039270456859374 0.5246157299496054 chr8 146364022 6028661 0.04118950079138984 0.5961152841777828 chr9 141213431 4906986 0.03474872018370547 0.3548199961113914 chr10 135534747 5384984 0.039731390799733445 0.3529263467120385 chr11 135006516 5127086 0.037976581811799366 0.2863131553984648 chr12 133851895 4946259 0.036953223561011224 0.23606177183573265 chr13 115169878 3853782 0.03346171817599737 0.21858700181875196 chr14 107349540 3505168 0.0326519144842167 0.22570686158025455 chr15 102531392 3228563 0.031488531824477715 0.211543425161563 chr16 90354753 2933147 0.032462564531607986 0.24432136936532547 chr17 81195210 2679014 0.032994729615207594 0.24330209073872097 chr18 78077248 3177196 0.040692981391967094 0.6901430282586123 chr19 59128983 1889644 0.03195799934526187 0.5201550465718635 chr20 63025520 2215560 0.03515337913911698 0.23170968839424116 chr21 48129895 1598632 0.033214948837931184 0.242262532122494 chr22 51304566 1168692 0.02277949295974943 0.17693892277832682 chrMT 16571 80434 4.853901394001569 3.5389114474276075 chrX 155270560 6781542 0.04367564591768072 0.27918611828701045 chrY 59373566 313919 0.005287184535959993 0.152708082810881