BamQC report ----------------------------------- >>>>>>> Input bam file = SRR619719.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP016866/SRP016866.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 = 14,643,235 number of mapped reads = 3,546,110 (24.22%) number of supplementary alignments = 52 (0%) number of secondary alignments = 0 number of mapped bases = 150,786,575 bp number of sequenced bases = 150,747,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 770,389 duplication rate = 13.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8899 >>>>>>> ACTG content number of A's = 36,128,251 bp (23.97%) number of C's = 24,967,802 bp (16.56%) number of T's = 55,469,294 bp (36.8%) number of G's = 34,173,409 bp (22.67%) number of N's = 9,091 bp (0.01%) GC percentage = 39.23% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,358,703 number of insertions = 11,048 mapped reads with insertion percentage = 0.31% number of deletions = 27,049 mapped reads with deletion percentage = 0.76% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.5743X There is a 3.29% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 11888838 0.04769832850286058 0.7548575539116326 chr2 243199373 13295411 0.054668771699505986 0.5874522809062517 chr3 198022430 10854809 0.0548160579586868 0.47788329452474665 chr4 191154276 11211772 0.05865300130665139 0.5583979856415218 chr5 180915260 9346368 0.05166157901771249 0.4553398587547611 chr6 171115067 9349772 0.05464026145634505 0.4979031071092227 chr7 159138663 8432610 0.05298907154950774 0.7817628822450303 chr8 146364022 8093687 0.055298336909599274 0.8880543296119904 chr9 141213431 6341679 0.04490846908181135 0.5157830282647998 chr10 135534747 7287852 0.05377109679483151 0.6775159478420788 chr11 135006516 6948926 0.0514710415903185 0.6374977981410279 chr12 133851895 7233002 0.05403735225414627 0.45649675792064703 chr13 115169878 5350858 0.04646056844828819 0.43853481713851655 chr14 107349540 4664548 0.043451960762943186 0.39344199773930255 chr15 102531392 4138462 0.04036287735174804 0.39461261737772224 chr16 90354753 3775789 0.04178849340665012 0.38914509626629523 chr17 81195210 3321593 0.04090873094607428 0.40993959525620716 chr18 78077248 4200364 0.05379754163466417 0.7771763043195654 chr19 59128983 2207357 0.037331218769651425 0.525846761758191 chr20 63025520 2764071 0.04385637754357283 0.45852904676886436 chr21 48129895 1988180 0.04130862949108865 0.439624941989388 chr22 51304566 1300880 0.02535602776563786 0.2936891215702203 chrMT 16571 42822 2.5841530384406495 3.2073403420186812 chrX 155270560 5489203 0.0353525033979397 0.4879835048184584 chrY 59373566 1257722 0.02118319792346648 0.2968985031751066