BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472615.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 = 19,549,616 number of mapped reads = 19,381,671 (99.14%) number of supplementary alignments = 99,545 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,720,430 number of mapped paired reads (second in pair) = 9,661,241 number of mapped paired reads (both in pair) = 19,281,874 number of mapped paired reads (singletons) = 99,797 number of mapped bases = 1,900,856,579 bp number of sequenced bases = 1,900,616,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,799,616 duplication rate = 50.59% >>>>>>> Insert size mean insert size = 20,282.56 std insert size = 1,438,559.6336 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 54.6105 >>>>>>> ACTG content number of A's = 498,203,168 bp (26.21%) number of C's = 454,377,656 bp (23.91%) number of T's = 498,842,343 bp (26.25%) number of G's = 448,832,220 bp (23.62%) number of N's = 360,857 bp (0.02%) GC percentage = 47.52% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 10,835,005 number of insertions = 106,245 mapped reads with insertion percentage = 0.54% number of deletions = 93,295 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.614X std coverageData = 25.9917X There is a 3.71% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% 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 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 302666801 1.2143071089881057 40.72348693787506 chr2 243199373 122944344 0.5055290335801976 31.695659310585413 chr3 198022430 141509052 0.7146112286370792 20.97771610135048 chr4 191154276 27467431 0.14369247486778688 7.794590292009207 chr5 180915260 112441086 0.6215124473192587 31.951019025272977 chr6 171115067 189804853 1.1092234969583363 34.080738923894636 chr7 159138663 74285231 0.46679562087309984 16.423457395026176 chr8 146364022 84966583 0.5805154971759385 20.453725618834003 chr9 141213431 89797118 0.6358964396240752 19.1143841743308 chr10 135534747 48970106 0.3613103435386942 23.63930928893238 chr11 135006516 50929840 0.37723986596321024 22.883901950950364 chr12 133851895 53650940 0.40082316354206265 14.65520500422643 chr13 115169878 82769398 0.7186722729705418 32.48380158473824 chr14 107349540 23058554 0.2147988151602699 9.508016740825655 chr15 102531392 43929349 0.42844779674892153 18.741848052323896 chr16 90354753 82145353 0.9091425771480998 29.927530324217646 chr17 81195210 98524032 1.2134217277102923 32.23830520807556 chr18 78077248 8753881 0.1121182063179276 3.410587221599506 chr19 59128983 69053322 1.1678422069258318 42.30542271842512 chr20 63025520 54314072 0.8617790380785434 28.01755891170713 chr21 48129895 14701146 0.3054472900886237 19.92759788603757 chr22 51304566 30237636 0.5893751445046821 28.90603505038233 chrMT 16571 4844 0.2923179047733993 0.7138386588563962 chrX 155270560 93602829 0.6028369383094903 21.147920811295773 chrY 59373566 328778 0.005537447422309113 0.43386159560365417