BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365345.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 560,350,488 number of mapped reads = 535,437,395 (95.55%) number of supplementary alignments = 2,333,285 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 268,262,078 number of mapped paired reads (second in pair) = 267,175,317 number of mapped paired reads (both in pair) = 532,066,586 number of mapped paired reads (singletons) = 3,370,809 number of mapped bases = 54,325,465,345 bp number of sequenced bases = 54,307,697,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 407,023,909 duplication rate = 44.48% >>>>>>> Insert size mean insert size = 64,598.0189 std insert size = 2,493,646.1208 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 53.7934 >>>>>>> ACTG content number of A's = 16,042,742,889 bp (29.54%) number of C's = 10,852,718,111 bp (19.98%) number of T's = 15,479,623,989 bp (28.5%) number of G's = 11,910,617,980 bp (21.93%) number of N's = 21,994,910 bp (0.04%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 337,940,098 number of insertions = 15,487,613 mapped reads with insertion percentage = 2.83% number of deletions = 8,506,679 mapped reads with deletion percentage = 1.55% homopolymer indels = 49.87% >>>>>>> Coverage mean coverageData = 17.5487X std coverageData = 144.5366X There is a 73.53% of reference with a coverageData >= 1X There is a 68.9% of reference with a coverageData >= 2X There is a 64.6% of reference with a coverageData >= 3X There is a 61.52% of reference with a coverageData >= 4X There is a 58.45% of reference with a coverageData >= 5X There is a 56.05% of reference with a coverageData >= 6X There is a 53.54% of reference with a coverageData >= 7X There is a 51.47% of reference with a coverageData >= 8X There is a 49.28% of reference with a coverageData >= 9X There is a 47.4% of reference with a coverageData >= 10X There is a 45.42% of reference with a coverageData >= 11X There is a 43.69% of reference with a coverageData >= 12X There is a 41.88% of reference with a coverageData >= 13X There is a 40.27% of reference with a coverageData >= 14X There is a 38.59% of reference with a coverageData >= 15X There is a 37.08% of reference with a coverageData >= 16X There is a 35.53% of reference with a coverageData >= 17X There is a 34.11% of reference with a coverageData >= 18X There is a 32.66% of reference with a coverageData >= 19X There is a 31.34% of reference with a coverageData >= 20X There is a 29.99% of reference with a coverageData >= 21X There is a 28.76% of reference with a coverageData >= 22X There is a 27.51% of reference with a coverageData >= 23X There is a 26.36% of reference with a coverageData >= 24X There is a 25.2% of reference with a coverageData >= 25X There is a 24.14% of reference with a coverageData >= 26X There is a 23.07% of reference with a coverageData >= 27X There is a 22.09% of reference with a coverageData >= 28X There is a 21.11% of reference with a coverageData >= 29X There is a 20.2% of reference with a coverageData >= 30X There is a 19.31% of reference with a coverageData >= 31X There is a 18.48% of reference with a coverageData >= 32X There is a 17.66% of reference with a coverageData >= 33X There is a 16.9% of reference with a coverageData >= 34X There is a 16.16% of reference with a coverageData >= 35X There is a 15.46% of reference with a coverageData >= 36X There is a 14.78% of reference with a coverageData >= 37X There is a 14.16% of reference with a coverageData >= 38X There is a 13.54% of reference with a coverageData >= 39X There is a 12.96% of reference with a coverageData >= 40X There is a 12.4% of reference with a coverageData >= 41X There is a 11.88% of reference with a coverageData >= 42X There is a 11.37% of reference with a coverageData >= 43X There is a 10.89% of reference with a coverageData >= 44X There is a 10.43% of reference with a coverageData >= 45X There is a 10% of reference with a coverageData >= 46X There is a 9.57% of reference with a coverageData >= 47X There is a 9.18% of reference with a coverageData >= 48X There is a 8.79% of reference with a coverageData >= 49X There is a 8.44% of reference with a coverageData >= 50X There is a 8.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4731203470 18.981711865022795 402.12915799869603 chr2 243199373 4745743218 19.513797093547605 95.63787409953126 chr3 198022430 3626651588 18.31434746053768 29.836647818470702 chr4 191154276 3388343608 17.72570134920759 78.41393797175394 chr5 180915260 3323422614 18.370051337847343 25.8651803990845 chr6 171115067 3209894853 18.75869208525045 52.16145995307703 chr7 159138663 2929435423 18.4080685848165 103.92218657515467 chr8 146364022 2717613753 18.567498459423312 44.168188730880836 chr9 141213431 2316835583 16.406623411055 121.79859754437908 chr10 135534747 2795077449 20.622589489911395 249.30501051470773 chr11 135006516 2567005099 19.013934845929956 78.49331671557266 chr12 133851895 2568105792 19.186174330964832 39.355007653872775 chr13 115169878 1697157739 14.736125178495023 22.69444280030895 chr14 107349540 1703892846 15.872381437312168 26.263733670867815 chr15 102531392 1652269614 16.114768187288437 28.274851219379663 chr16 90354753 1618680358 17.914722848060908 53.44153363204832 chr17 81195210 1695831601 20.88585768791041 67.25663034256512 chr18 78077248 1403232677 17.972363434223503 146.8374228641431 chr19 59128983 1221001065 20.64978971480027 199.96074201387978 chr20 63025520 1154468016 18.317469114098543 32.25421526093687 chr21 48129895 713937616 14.833558560640949 49.921778401274416 chr22 51304566 739250973 14.409067859574137 38.768520707733494 chrMT 16571 59668209 3600.7609076096796 804.6115328577293 chrX 155270560 1336202935 8.605642531333693 31.182772989709846 chrY 59373566 410539246 6.9145121921765655 135.39559777063351