BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472824.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,230,947 number of mapped reads = 1,315,913 (58.98%) number of supplementary alignments = 6,529 (0.29%) number of secondary alignments = 0 number of mapped bases = 80,701,541 bp number of sequenced bases = 80,657,569 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,085 duplication rate = 7.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3782 >>>>>>> ACTG content number of A's = 21,621,175 bp (26.81%) number of C's = 15,374,548 bp (19.06%) number of T's = 24,649,788 bp (30.56%) number of G's = 19,010,247 bp (23.57%) number of N's = 1,811 bp (0%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 790,110 number of insertions = 5,749 mapped reads with insertion percentage = 0.43% number of deletions = 24,798 mapped reads with deletion percentage = 1.86% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 0.0261X std coverageData = 0.2743X There is a 1.83% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6437826 0.025828726019503076 0.3401782100865756 chr2 243199373 8001765 0.032902079069093655 0.3162524619149717 chr3 198022430 5279634 0.02666179785794973 0.23189094407278565 chr4 191154276 4649925 0.024325508679701208 0.22631266030318709 chr5 180915260 4285603 0.023688455025850225 0.22490415906536243 chr6 171115067 4631949 0.027069206009778204 0.264838175420863 chr7 159138663 4835736 0.03038693368939514 0.4076712033009602 chr8 146364022 4220627 0.02883650600965311 0.27657075627695304 chr9 141213431 3342447 0.023669469513845322 0.26845529027610476 chr10 135534747 3886315 0.028673938499328148 0.2690893331239816 chr11 135006516 3461793 0.025641673473004813 0.2700882669862989 chr12 133851895 3953192 0.02953407570359762 0.24480249661001327 chr13 115169878 2153048 0.018694540945853915 0.20563605469522683 chr14 107349540 2786789 0.025959952879164642 0.243497932829421 chr15 102531392 2572858 0.025093368477821894 0.23994580258411963 chr16 90354753 2423585 0.026822994026667307 0.23845570546021244 chr17 81195210 1993664 0.02455396075704466 0.23687837746051174 chr18 78077248 1752038 0.0224398021815523 0.3674702485783905 chr19 59128983 1548450 0.026187665023766772 0.2764812858703826 chr20 63025520 1776039 0.028179680231119077 0.24731208110600972 chr21 48129895 1254175 0.026058128736827703 0.2341158301580282 chr22 51304566 902288 0.017586894702510493 0.19066025443545592 chrMT 16571 147747 8.915997827530022 6.682790376158727 chrX 155270560 4201308 0.027057981886585585 0.2519288291259784 chrY 59373566 202740 0.0034146508902631856 0.08256695982619867