BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054566.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,441,281 number of mapped reads = 9,809,568 (72.98%) number of supplementary alignments = 260 (0%) number of secondary alignments = 0 number of mapped bases = 464,417,793 bp number of sequenced bases = 464,321,295 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,304,944 duplication rate = 22.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5569 >>>>>>> ACTG content number of A's = 138,542,702 bp (29.84%) number of C's = 90,551,195 bp (19.5%) number of T's = 137,694,066 bp (29.65%) number of G's = 97,314,394 bp (20.96%) number of N's = 218,938 bp (0.05%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 3,031,193 number of insertions = 20,370 mapped reads with insertion percentage = 0.21% number of deletions = 64,677 mapped reads with deletion percentage = 0.66% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 0.15X std coverageData = 1.3691X There is a 4.4% of reference with a coverageData >= 1X There is a 2.23% of reference with a coverageData >= 2X There is a 1.51% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.86% of reference with a coverageData >= 5X There is a 0.68% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% 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 0.04% 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 0.03% 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 39694703 0.15925618496252414 1.513138502823285 chr2 243199373 44044931 0.18110626872380958 1.5800722473794044 chr3 198022430 29796430 0.15046997453773292 1.2978726985874212 chr4 191154276 23392489 0.12237491878026312 1.1863000172799116 chr5 180915260 23622474 0.13057203687516464 1.2052745192250012 chr6 171115067 30033835 0.17551835455845627 1.511420086801026 chr7 159138663 24595011 0.1545508208775136 1.3917905193899087 chr8 146364022 26090167 0.17825532971483934 1.5294757451303058 chr9 141213431 24617337 0.1743271643899085 1.4692970030469124 chr10 135534747 16194729 0.11948765433560739 1.2182671290550515 chr11 135006516 21205059 0.15706693001395577 1.4066893886081464 chr12 133851895 24894575 0.18598597352693438 1.4776892557756394 chr13 115169878 12064023 0.10474981140467997 1.0868002251823365 chr14 107349540 9138719 0.08513049054518539 1.0395136325305454 chr15 102531392 14081065 0.1373341834664646 1.225484290709294 chr16 90354753 11394629 0.12610990149018503 1.1864711322069355 chr17 81195210 10438476 0.12856024388630807 1.1653506399665665 chr18 78077248 14493453 0.18562966000031147 1.5906798500067745 chr19 59128983 9542754 0.16138877274449318 1.4368501420965176 chr20 63025520 9950006 0.15787265222087815 1.3642947683176565 chr21 48129895 5316409 0.11045960104421587 1.179227742558061 chr22 51304566 7361765 0.14349141945767557 1.2840827016105754 chrMT 16571 28412 1.7145615834892283 4.820632614366267 chrX 155270560 31270999 0.20139683272862544 1.6168199863526134 chrY 59373566 1155343 0.01945887838369014 0.43225618185207626