BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083619.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,695,659 number of mapped reads = 1,501,090 (88.53%) number of supplementary alignments = 17,842 (1.05%) number of secondary alignments = 0 number of mapped bases = 98,934,679 bp number of sequenced bases = 98,898,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,184 duplication rate = 5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7825 >>>>>>> ACTG content number of A's = 26,346,524 bp (26.64%) number of C's = 18,624,662 bp (18.83%) number of T's = 30,956,774 bp (31.3%) number of G's = 22,966,008 bp (23.22%) number of N's = 4,927 bp (0%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 694,109 number of insertions = 7,074 mapped reads with insertion percentage = 0.47% number of deletions = 22,085 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.032X std coverageData = 0.276X There is a 2.56% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 10837440 0.043480092272267595 0.4544439685933267 chr2 243199373 9070093 0.037294886446931755 0.43320909387517875 chr3 198022430 9010259 0.04550120408077004 0.2615998627630577 chr4 191154276 2700094 0.014125208478203229 0.1471859071958657 chr5 180915260 4305803 0.023800109509833498 0.18505709817985969 chr6 171115067 6380452 0.037287493800881956 0.254028489415813 chr7 159138663 7926916 0.049811377389792445 0.3479437706794542 chr8 146364022 6452426 0.044084781982829085 0.2784892995165331 chr9 141213431 3838136 0.027179680946920692 0.21525033308274286 chr10 135534747 4560014 0.0336446121819964 0.23694694131122473 chr11 135006516 3530078 0.026147463875002892 0.21019050094019034 chr12 133851895 3133133 0.02340746091043388 0.18459348914797039 chr13 115169878 3410121 0.029609486952829802 0.20932010855411853 chr14 107349540 2446353 0.02278866774836669 0.18310102846669377 chr15 102531392 2613493 0.025489686124616353 0.2014554185493047 chr16 90354753 2737076 0.03029255140567979 0.2166296804558577 chr17 81195210 2124314 0.026163045824993864 0.1950308495894629 chr18 78077248 2341644 0.029991374695993382 0.29701110712690254 chr19 59128983 3159929 0.053441287836795706 0.38243643942243166 chr20 63025520 1702348 0.027010455447253747 0.19952282262308968 chr21 48129895 948450 0.01970604756149998 0.16973965136127891 chr22 51304566 833490 0.01624592243895017 0.1527126586500164 chrMT 16571 12993 0.7840806227747269 1.1175471081928687 chrX 155270560 4685840 0.03017854769120431 0.21423139397084584 chrY 59373566 173784 0.0029269591117366944 0.06670144573596591