BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212689.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 = 3,058,752 number of mapped reads = 2,582,162 (84.42%) number of supplementary alignments = 12,023 (0.39%) number of secondary alignments = 0 number of mapped bases = 172,659,971 bp number of sequenced bases = 172,594,048 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,755 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7503 >>>>>>> ACTG content number of A's = 47,752,213 bp (27.67%) number of C's = 30,514,370 bp (17.68%) number of T's = 56,849,629 bp (32.94%) number of G's = 37,430,202 bp (21.69%) number of N's = 47,634 bp (0.03%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,684,748 number of insertions = 15,184 mapped reads with insertion percentage = 0.58% number of deletions = 40,462 mapped reads with deletion percentage = 1.55% homopolymer indels = 49.61% >>>>>>> Coverage mean coverageData = 0.0558X std coverageData = 0.3789X There is a 4.69% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.12% 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 0.01% 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 13640165 0.05472469815832475 0.5798234030730848 chr2 243199373 15431646 0.0634526553651929 0.43127759653588355 chr3 198022430 12504117 0.06314495282175862 0.28779557185455595 chr4 191154276 12169488 0.0636631743461496 0.3055524987373826 chr5 180915260 10919488 0.06035692069314662 0.2816343183454758 chr6 171115067 10782181 0.06301128935653574 0.3390982465654036 chr7 159138663 9745495 0.06123901518514077 0.5671798394360632 chr8 146364022 9086286 0.062080051339392685 0.41124089384380014 chr9 141213431 7447661 0.052740457810985415 0.38237292925809097 chr10 135534747 7720317 0.056961902175535845 0.3332811364383286 chr11 135006516 8264656 0.061216719347086924 0.3596069325838173 chr12 133851895 8058274 0.06020291307792094 0.2832880632902552 chr13 115169878 6011115 0.052193465030847735 0.2617490408205441 chr14 107349540 5316740 0.049527366395794525 0.27559545564013577 chr15 102531392 4817750 0.046988048304269586 0.2480798001368264 chr16 90354753 4910467 0.05434652673999341 0.29713056027185925 chr17 81195210 4370043 0.053821438481407954 0.30496339169231845 chr18 78077248 4851174 0.06213300448294489 0.6762595062257515 chr19 59128983 3094558 0.05233572172212061 0.4541816999153033 chr20 63025520 3444385 0.05465063993125324 0.2801041871412688 chr21 48129895 2354556 0.048920863010401335 0.27248190507154707 chr22 51304566 1836550 0.035797008788652454 0.21564649040019482 chrMT 16571 41084 2.4792710156297146 2.5873560558262434 chrX 155270560 5494641 0.03538752613502521 0.23650519986457946 chrY 59373566 347134 0.005846608573249584 0.15681976467824732