BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004083.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 = 3,004,468 number of mapped reads = 2,774,175 (92.33%) number of supplementary alignments = 16,836 (0.56%) number of secondary alignments = 0 number of mapped bases = 186,591,734 bp number of sequenced bases = 186,512,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,725 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3005 >>>>>>> ACTG content number of A's = 52,072,338 bp (27.92%) number of C's = 34,205,552 bp (18.34%) number of T's = 59,027,631 bp (31.65%) number of G's = 41,123,668 bp (22.05%) number of N's = 83,407 bp (0.04%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,379,361 number of insertions = 12,906 mapped reads with insertion percentage = 0.46% number of deletions = 45,575 mapped reads with deletion percentage = 1.63% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.0603X std coverageData = 0.4625X There is a 4.87% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 16579918 0.06651906395852068 0.8451335402302275 chr2 243199373 18753747 0.07711264535209143 0.6007632943483004 chr3 198022430 9884029 0.04991368402054252 0.2614051086638868 chr4 191154276 11009971 0.057597304284210726 0.3035342534332022 chr5 180915260 10609888 0.05864562226536335 0.2879361915429754 chr6 171115067 12935122 0.07559312120656213 0.3815205040249253 chr7 159138663 11889214 0.07470977684410984 0.5193862717917395 chr8 146364022 11031495 0.07537026414865806 0.6258419223575202 chr9 141213431 5916239 0.041895724493798324 0.40330491633265525 chr10 135534747 5597794 0.04130154166296559 0.38547006446971255 chr11 135006516 9736946 0.07212204483522855 0.4786536664239291 chr12 133851895 9105224 0.06802461780612071 0.3148062661849046 chr13 115169878 4566262 0.039648057975714794 0.23459882544916288 chr14 107349540 3506901 0.03266805800937759 0.23027926265799506 chr15 102531392 4422746 0.04313553062851229 0.2556192915892649 chr16 90354753 4779333 0.052895202978419965 0.28704383522224425 chr17 81195210 5449150 0.06711171755082597 0.3414697063366312 chr18 78077248 6171064 0.07903792920570152 0.7209134560351848 chr19 59128983 2044759 0.03458133213622159 0.5897762566541387 chr20 63025520 5235847 0.08307503055904973 0.37378560699003294 chr21 48129895 2364524 0.04912796921746868 0.28529620126040023 chr22 51304566 1245409 0.024274817956748723 0.17833146632587135 chrMT 16571 24429 1.474201919015147 1.663688044838238 chrX 155270560 13291285 0.08560080545854926 0.39590449386185744 chrY 59373566 440438 0.007418082316295437 0.15343835057487615