BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472810.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 = 2,334,631 number of mapped reads = 1,839,221 (78.78%) number of supplementary alignments = 16,936 (0.73%) number of secondary alignments = 0 number of mapped bases = 117,330,261 bp number of sequenced bases = 117,280,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,199 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1799 >>>>>>> ACTG content number of A's = 31,261,475 bp (26.66%) number of C's = 23,894,345 bp (20.37%) number of T's = 34,308,339 bp (29.25%) number of G's = 27,813,462 bp (23.72%) number of N's = 2,922 bp (0%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,031,999 number of insertions = 9,190 mapped reads with insertion percentage = 0.5% number of deletions = 27,519 mapped reads with deletion percentage = 1.48% homopolymer indels = 44.89% >>>>>>> Coverage mean coverageData = 0.0379X std coverageData = 0.2982X There is a 3.16% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 9670646 0.03879888427640066 0.361258462121152 chr2 243199373 10198266 0.04193376764996841 0.40065534560746446 chr3 198022430 8512480 0.04298745349201098 0.2445942182543527 chr4 191154276 5561158 0.029092511642271605 0.2231579028707483 chr5 180915260 6557297 0.036245129349508715 0.22685393705866919 chr6 171115067 7805213 0.045613826630474336 0.27047577523339356 chr7 159138663 6406174 0.04025529609985475 0.3727009784306172 chr8 146364022 6083010 0.04156082838445093 0.28868271244377974 chr9 141213431 5618662 0.039788439103926314 0.32942097001242787 chr10 135534747 5523129 0.040750649720842434 0.2940653838630798 chr11 135006516 4538452 0.03361654040461277 0.3150087951080559 chr12 133851895 5515512 0.041206080795494156 0.24618620434413063 chr13 115169878 5588692 0.04852563966421845 0.26332901915198176 chr14 107349540 2954919 0.027526144965316107 0.22019927700181155 chr15 102531392 2756782 0.0268871995807879 0.20704066087194167 chr16 90354753 3594359 0.03978051934910386 0.25512583316671145 chr17 81195210 3058953 0.037674057373581524 0.24952624596739825 chr18 78077248 2508374 0.032126823937237134 0.5252335121208311 chr19 59128983 2751183 0.046528501936182465 0.3177404402460384 chr20 63025520 3698120 0.05867654880118403 0.2948745694580756 chr21 48129895 1592409 0.033085652898266246 0.24602239090661857 chr22 51304566 1314080 0.025613314807107032 0.19512206303785243 chrMT 16571 108583 6.552591877376139 5.031731817768011 chrX 155270560 5105039 0.03287834474223575 0.24273217368624336 chrY 59373566 308769 0.005200445598972445 0.11853576351261176