BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083751.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,173,120 number of mapped reads = 1,800,776 (82.87%) number of supplementary alignments = 13,582 (0.62%) number of secondary alignments = 0 number of mapped bases = 108,603,636 bp number of sequenced bases = 108,570,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,860 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4408 >>>>>>> ACTG content number of A's = 32,296,782 bp (29.75%) number of C's = 20,865,520 bp (19.22%) number of T's = 32,090,388 bp (29.56%) number of G's = 23,311,721 bp (21.47%) number of N's = 6,337 bp (0.01%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 894,588 number of insertions = 7,610 mapped reads with insertion percentage = 0.42% number of deletions = 21,111 mapped reads with deletion percentage = 1.16% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.2833X There is a 3.12% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 10837295 0.04347951052848129 0.561585925380314 chr2 243199373 9598296 0.03946677938186954 0.2560593558060924 chr3 198022430 9688809 0.04892783610422314 0.24469980426462765 chr4 191154276 5599026 0.029290613410081393 0.18997718656363008 chr5 180915260 5472956 0.030251489012038012 0.19047048771859762 chr6 171115067 7538389 0.04405450164128446 0.26311208475532843 chr7 159138663 7606017 0.047794903241081016 0.40569348322809856 chr8 146364022 7539247 0.05151024751150935 0.3731360775792591 chr9 141213431 4228083 0.0299410825872505 0.2106403189150614 chr10 135534747 4801606 0.03542712187303526 0.2526562230679723 chr11 135006516 3765496 0.02789121674690131 0.19781115769894123 chr12 133851895 3832854 0.02863503725516923 0.1854929524808332 chr13 115169878 3577964 0.031066838500949007 0.1919956946509089 chr14 107349540 2207193 0.020560805383982084 0.15768887954683108 chr15 102531392 2693431 0.026269330274965936 0.1783924138696119 chr16 90354753 2709002 0.029981842792487078 0.1938402661251143 chr17 81195210 2077301 0.025584033836478778 0.17751031013148488 chr18 78077248 2563612 0.03283430276640898 0.3128931553043118 chr19 59128983 2758833 0.04665788011270209 0.4014773710817903 chr20 63025520 1975968 0.031351871432397545 0.1954726329758806 chr21 48129895 1753272 0.03642792073408845 0.2106630327947607 chr22 51304566 701773 0.013678568102495984 0.1270777664223417 chrMT 16571 5641 0.34041397622352304 0.6709040377417423 chrX 155270560 4847237 0.03121800423724884 0.1977088266985161 chrY 59373566 224335 0.003778364937689611 0.07899126468951898