BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549129.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,691,086 number of mapped reads = 11,994,780 (87.61%) number of secondary alignments = 0 number of mapped bases = 475,807,165 bp number of sequenced bases = 475,761,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 697,114 duplication rate = 4.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8647 >>>>>>> ACTG content number of A's = 135,353,287 bp (28.45%) number of C's = 101,609,918 bp (21.36%) number of T's = 136,870,302 bp (28.77%) number of G's = 101,812,771 bp (21.4%) number of N's = 114,749 bp (0.02%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 1,601,845 number of insertions = 12,545 mapped reads with insertion percentage = 0.1% number of deletions = 36,814 mapped reads with deletion percentage = 0.31% homopolymer indels = 45.69% >>>>>>> Coverage mean coverageData = 0.1537X std coverageData = 0.8664X There is a 10.5% of reference with a coverageData >= 1X There is a 3.05% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 39066590 0.1567361792049457 1.5781479334506494 chr2 243199373 40399197 0.16611554751006696 0.8336085055509004 chr3 198022430 32321188 0.1632198332279833 0.5602068588013029 chr4 191154276 29554441 0.15461041007526297 0.5799645563934737 chr5 180915260 28883638 0.15965285625988654 0.5697795289487799 chr6 171115067 27322422 0.1596728007592692 0.6217781094501799 chr7 159138663 26353976 0.16560385454539103 1.180568310407631 chr8 146364022 23719195 0.16205618481842485 1.024671279096482 chr9 141213431 20566914 0.14564417742955343 0.7907256948963621 chr10 135534747 23071589 0.17022637744695832 0.8176860146414356 chr11 135006516 22031901 0.1631913899622445 0.7539375214198949 chr12 133851895 22071268 0.16489320528484114 0.5889819382256986 chr13 115169878 14827753 0.12874679783892798 0.4914979747864531 chr14 107349540 14828980 0.1381373408772874 0.6979608456087484 chr15 102531392 14494469 0.1413661583761586 0.5104103478056078 chr16 90354753 15077676 0.1668719740731293 0.6197762476399671 chr17 81195210 14665517 0.1806204700991598 0.6470657475895685 chr18 78077248 12559312 0.1608575138304055 1.5503618365048812 chr19 59128983 11173365 0.18896595938408073 1.3757603892518784 chr20 63025520 11022233 0.1748852369643281 0.6171794328906026 chr21 48129895 6334216 0.13160668644716553 0.5957136564190784 chr22 51304566 6684050 0.13028177647969968 0.540695003479068 chrMT 16571 267320 16.13179651197876 20.31724895719452 chrX 155270560 14846579 0.09561747571464932 0.539468045535536 chrY 59373566 3663376 0.061700454373921215 0.5243307314213692