BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472506.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 = 17,382,590 number of mapped reads = 17,120,833 (98.49%) number of supplementary alignments = 69,295 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,605,884 number of mapped paired reads (second in pair) = 8,514,949 number of mapped paired reads (both in pair) = 16,977,146 number of mapped paired reads (singletons) = 143,687 number of mapped bases = 1,686,673,477 bp number of sequenced bases = 1,686,448,689 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,760,582 duplication rate = 45.57% >>>>>>> Insert size mean insert size = 30,396.5975 std insert size = 1,670,269.7086 median insert size = 246 >>>>>>> Mapping quality mean mapping quality = 54.983 >>>>>>> ACTG content number of A's = 469,582,077 bp (27.84%) number of C's = 376,326,825 bp (22.31%) number of T's = 466,217,894 bp (27.64%) number of G's = 374,063,065 bp (22.18%) number of N's = 258,828 bp (0.02%) GC percentage = 44.5% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 11,129,284 number of insertions = 91,815 mapped reads with insertion percentage = 0.53% number of deletions = 89,957 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.59% >>>>>>> Coverage mean coverageData = 0.5448X std coverageData = 18.9698X There is a 5.25% of reference with a coverageData >= 1X There is a 2.29% of reference with a coverageData >= 2X There is a 1.02% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 153113947 0.6142971535465102 18.340525932616533 chr2 243199373 108749303 0.4471611158306728 17.928829652895644 chr3 198022430 184609368 0.932264935845904 20.22499876455921 chr4 191154276 71729715 0.3752451501529581 13.536908145357508 chr5 180915260 89200137 0.49304927069170396 18.012630287871467 chr6 171115067 80606947 0.4710686698325636 13.3914659545595 chr7 159138663 86303896 0.5423188455466664 23.40891747227682 chr8 146364022 115138455 0.7866581788795063 31.64678296329801 chr9 141213431 106558879 0.7545945045411439 21.795707492490276 chr10 135534747 50667725 0.37383568510295 13.40430409733484 chr11 135006516 76409426 0.5659684307385578 18.00025569056632 chr12 133851895 122624014 0.9161171308034152 32.14893440921411 chr13 115169878 41412515 0.35957765797060237 14.521810387497109 chr14 107349540 23793527 0.22164535590930337 7.127515978237362 chr15 102531392 43309132 0.42239875178911057 14.569589228884405 chr16 90354753 49815275 0.5513298785731836 18.26739720460518 chr17 81195210 66126761 0.8144170204129036 17.749775657886453 chr18 78077248 27884292 0.35713722901708833 13.38620282245563 chr19 59128983 36765768 0.6217892839455736 17.821475535130386 chr20 63025520 38474999 0.6104669822636926 26.048977046517294 chr21 48129895 4983422 0.1035410943655705 3.508174107012039 chr22 51304566 19423689 0.37859571797176883 12.1287181542013 chrMT 16571 3136 0.1892462736105244 0.7241001476551793 chrX 155270560 86733837 0.5585980819544929 17.598915846844065 chrY 59373566 2235312 0.03764826926514739 1.4104955804135788