BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514748.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 53,328,309 number of mapped reads = 49,932,423 (93.63%) number of supplementary alignments = 7,183,418 (13.47%) number of secondary alignments = 0 number of mapped bases = 4,692,679,026 bp number of sequenced bases = 4,687,966,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,712,070 duplication rate = 42.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6449 >>>>>>> ACTG content number of A's = 1,453,724,581 bp (31.01%) number of C's = 876,114,416 bp (18.69%) number of T's = 1,440,485,890 bp (30.73%) number of G's = 917,319,086 bp (19.57%) number of N's = 322,117 bp (0.01%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 28,478,106 number of insertions = 3,623,455 mapped reads with insertion percentage = 6.86% number of deletions = 1,637,166 mapped reads with deletion percentage = 2.99% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 1.5159X std coverageData = 56.2658X There is a 5.43% of reference with a coverageData >= 1X There is a 3.54% of reference with a coverageData >= 2X There is a 2.85% of reference with a coverageData >= 3X There is a 2.47% of reference with a coverageData >= 4X There is a 2.21% of reference with a coverageData >= 5X There is a 2.02% of reference with a coverageData >= 6X There is a 1.87% of reference with a coverageData >= 7X There is a 1.74% of reference with a coverageData >= 8X There is a 1.64% of reference with a coverageData >= 9X There is a 1.55% of reference with a coverageData >= 10X There is a 1.47% of reference with a coverageData >= 11X There is a 1.4% of reference with a coverageData >= 12X There is a 1.34% of reference with a coverageData >= 13X There is a 1.29% of reference with a coverageData >= 14X There is a 1.23% of reference with a coverageData >= 15X There is a 1.19% of reference with a coverageData >= 16X There is a 1.15% of reference with a coverageData >= 17X There is a 1.11% of reference with a coverageData >= 18X There is a 1.07% of reference with a coverageData >= 19X There is a 1.04% of reference with a coverageData >= 20X There is a 1.01% of reference with a coverageData >= 21X There is a 0.98% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.92% of reference with a coverageData >= 24X There is a 0.9% of reference with a coverageData >= 25X There is a 0.88% of reference with a coverageData >= 26X There is a 0.85% of reference with a coverageData >= 27X There is a 0.83% of reference with a coverageData >= 28X There is a 0.81% of reference with a coverageData >= 29X There is a 0.8% of reference with a coverageData >= 30X There is a 0.78% of reference with a coverageData >= 31X There is a 0.76% of reference with a coverageData >= 32X There is a 0.74% of reference with a coverageData >= 33X There is a 0.73% of reference with a coverageData >= 34X There is a 0.71% of reference with a coverageData >= 35X There is a 0.7% of reference with a coverageData >= 36X There is a 0.69% of reference with a coverageData >= 37X There is a 0.67% of reference with a coverageData >= 38X There is a 0.66% of reference with a coverageData >= 39X There is a 0.65% of reference with a coverageData >= 40X There is a 0.64% of reference with a coverageData >= 41X There is a 0.62% of reference with a coverageData >= 42X There is a 0.61% of reference with a coverageData >= 43X There is a 0.6% of reference with a coverageData >= 44X There is a 0.59% of reference with a coverageData >= 45X There is a 0.58% of reference with a coverageData >= 46X There is a 0.57% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.55% of reference with a coverageData >= 50X There is a 0.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 380648394 1.5271712963956867 45.02415434219262 chr2 243199373 354219660 1.4564990675366585 56.344843532265685 chr3 198022430 266180770 1.344195049015407 32.433666570706244 chr4 191154276 435200282 2.2766965568690707 98.97418612091793 chr5 180915260 362862462 2.0057040075005284 31.041199622178098 chr6 171115067 283757121 1.6582824994598517 46.0245010709092 chr7 159138663 257167302 1.615995114901776 58.46340547689585 chr8 146364022 245884837 1.6799540873507834 88.89388733484205 chr9 141213431 174684261 1.237022992522574 26.688292601689557 chr10 135534747 240679457 1.7757767829086661 54.956156151007356 chr11 135006516 168619796 1.2489752420542428 21.718907036681774 chr12 133851895 231013146 1.7258862565972637 28.132368565185104 chr13 115169878 138165544 1.1996673644127678 44.7026926990729 chr14 107349540 116485213 1.0851021159475858 25.03156724153667 chr15 102531392 117244136 1.1434950185792854 32.407844022417926 chr16 90354753 217307762 2.40505070054256 83.7933044534194 chr17 81195210 74836140 0.9216817100417624 28.4960186826649 chr18 78077248 110318933 1.4129459711489831 27.59471682690212 chr19 59128983 40061313 0.6775241339767335 24.460728979903433 chr20 63025520 81596895 1.2946643677037493 34.86125605654512 chr21 48129895 134947107 2.8038105422835433 176.7459704166422 chr22 51304566 34127056 0.6651855509312757 38.1163186215907 chrMT 16571 67918196 4098.617826323095 3070.4880035408387 chrX 155270560 132364865 0.8524788279246239 38.34296632877301 chrY 59373566 26388378 0.44444657408652194 11.091637412805271