BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080769.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 = 5,343,122 number of mapped reads = 3,499,178 (65.49%) number of supplementary alignments = 24,302 (0.45%) number of secondary alignments = 0 number of mapped bases = 221,483,506 bp number of sequenced bases = 221,409,298 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 368,246 duplication rate = 8.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3794 >>>>>>> ACTG content number of A's = 65,825,586 bp (29.73%) number of C's = 45,524,962 bp (20.56%) number of T's = 60,594,655 bp (27.37%) number of G's = 49,393,322 bp (22.31%) number of N's = 70,773 bp (0.03%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,954,136 number of insertions = 16,313 mapped reads with insertion percentage = 0.46% number of deletions = 40,439 mapped reads with deletion percentage = 1.14% homopolymer indels = 43.48% >>>>>>> Coverage mean coverageData = 0.0715X std coverageData = 0.4682X There is a 4.87% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% 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% 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 25829930 0.10363035364313095 0.6083512588157892 chr2 243199373 13710603 0.05637598004827093 0.43058462970762557 chr3 198022430 12809447 0.06468684885848537 0.3590092437823478 chr4 191154276 12029940 0.0629331462090861 0.4076823163576347 chr5 180915260 15857737 0.08765284365730121 0.4222653903316601 chr6 171115067 15986118 0.09342320509975899 0.6564838210545063 chr7 159138663 14770733 0.0928167468643368 0.591733967091734 chr8 146364022 9704335 0.06630273524459447 0.5438596280697465 chr9 141213431 9567634 0.06775300289956131 0.41632478132859546 chr10 135534747 9462806 0.0698183027559715 0.5341476262398299 chr11 135006516 11806235 0.0874493717029184 0.4796592132159662 chr12 133851895 8359219 0.06245125629338307 0.3636510274799714 chr13 115169878 9625463 0.08357621946946926 0.41460598189414977 chr14 107349540 6072256 0.056565272659761745 0.3669116311019635 chr15 102531392 7868111 0.0767385563242914 0.4011983248604471 chr16 90354753 5544693 0.06136581436949974 0.38201796868720467 chr17 81195210 5239391 0.0645283262399346 0.38006621689960696 chr18 78077248 3423354 0.04384573083313592 0.4921382448250692 chr19 59128983 3485835 0.05895306875141079 0.5990740584243037 chr20 63025520 3737730 0.059305024377426796 0.3621974907546289 chr21 48129895 2590982 0.0538331114165115 0.3932433725308394 chr22 51304566 1610215 0.031385413142370214 0.2508029912292056 chrMT 16571 39899 2.40776054553135 2.9483468716652945 chrX 155270560 11725736 0.07551808919862207 0.40729219714019466 chrY 59373566 625104 0.010528321644012422 0.2985784094891022