BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081163.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 = 2,537,739 number of mapped reads = 2,287,388 (90.13%) number of supplementary alignments = 20,418 (0.8%) number of secondary alignments = 0 number of mapped bases = 154,363,354 bp number of sequenced bases = 154,306,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,577 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0184 >>>>>>> ACTG content number of A's = 44,214,228 bp (28.65%) number of C's = 28,343,378 bp (18.37%) number of T's = 48,690,398 bp (31.55%) number of G's = 33,011,759 bp (21.39%) number of N's = 46,561 bp (0.03%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,268,498 number of insertions = 12,137 mapped reads with insertion percentage = 0.53% number of deletions = 35,113 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.3886X There is a 4.24% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 12350734 0.0495514673161035 0.6357458766776409 chr2 243199373 13332685 0.054822036897274405 0.45080637248421185 chr3 198022430 10288845 0.05195797768969909 0.2581688939713343 chr4 191154276 10942760 0.05724569823381822 0.28308829122443885 chr5 180915260 9483875 0.052421642043904974 0.26142564192607215 chr6 171115067 9399531 0.05493105408420873 0.3494000801546731 chr7 159138663 8283662 0.05205310792387391 0.49094160724951386 chr8 146364022 8129210 0.055541039996837474 0.5640364691267598 chr9 141213431 6384956 0.0452149342649992 0.3731572679186165 chr10 135534747 7107163 0.05243794050834802 0.3377548945183797 chr11 135006516 6948806 0.05147015274433124 0.33636534579516864 chr12 133851895 6814114 0.05090786350092391 0.26183152868603765 chr13 115169878 5029908 0.04367381547456358 0.23669980595025408 chr14 107349540 4789847 0.04461916650970279 0.2667576972354147 chr15 102531392 4271915 0.04166445921264777 0.23788906761858064 chr16 90354753 4565199 0.05052527784564914 0.2860818972527663 chr17 81195210 3333158 0.0410511654566815 0.2713642364672581 chr18 78077248 4230671 0.05418570849218456 0.6949330983152497 chr19 59128983 2528476 0.04276204107890711 0.4974368416610091 chr20 63025520 2420560 0.038406029811416074 0.23257528897447496 chr21 48129895 2073990 0.04309151308142268 0.25266203176726887 chr22 51304566 1432256 0.027916735520187422 0.18806217920862753 chrMT 16571 8930 0.5388932472391528 0.8663540071555409 chrX 155270560 9838137 0.06336125148257339 0.3192994559127472 chrY 59373566 373966 0.006298526856210725 0.13072298780160407