BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240273.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,062,042 number of mapped reads = 1,613,203 (78.23%) number of supplementary alignments = 14,791 (0.72%) number of secondary alignments = 0 number of mapped bases = 103,302,915 bp number of sequenced bases = 103,265,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,379 duplication rate = 10.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0299 >>>>>>> ACTG content number of A's = 28,901,460 bp (27.99%) number of C's = 18,699,168 bp (18.11%) number of T's = 32,920,431 bp (31.88%) number of G's = 22,717,134 bp (22%) number of N's = 26,822 bp (0.03%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 803,018 number of insertions = 7,364 mapped reads with insertion percentage = 0.45% number of deletions = 22,898 mapped reads with deletion percentage = 1.4% homopolymer indels = 48.17% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.3918X There is a 1.72% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.1% 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 7705734 0.030915606023705754 0.5314058275040809 chr2 243199373 9456414 0.03888338149621792 0.4634329519519286 chr3 198022430 7053807 0.03562125260254609 0.3320899148644443 chr4 191154276 6871763 0.035948779926848196 0.3386343219484017 chr5 180915260 6584895 0.03639767590638844 0.3335362907054617 chr6 171115067 5859133 0.03424089475417147 0.366239123052709 chr7 159138663 5412555 0.03401156512167002 0.4450286979257423 chr8 146364022 6265445 0.042807275410892985 0.549342236350172 chr9 141213431 4270456 0.030241146113077585 0.36446356969586946 chr10 135534747 4955973 0.036566069658875 0.3930377549080918 chr11 135006516 4671977 0.0346055667416823 0.3792710369353213 chr12 133851895 4873981 0.036413238676972035 0.33520474516334003 chr13 115169878 3267248 0.028368945567520704 0.2998938306447092 chr14 107349540 3081941 0.028709401083600358 0.3207573627333897 chr15 102531392 2767362 0.026990387490301505 0.3275442166298641 chr16 90354753 2683053 0.029694652587894298 0.2999626057399974 chr17 81195210 2517618 0.03100697688940025 0.31178950441063474 chr18 78077248 2466558 0.0315912517818251 0.5449151853961961 chr19 59128983 1734617 0.029336154826136617 0.41605710149172836 chr20 63025520 1977747 0.03138009809359764 0.31114685891182897 chr21 48129895 1275048 0.026491809300643602 0.2810078245897508 chr22 51304566 961133 0.01873386863851455 0.2272709397431581 chrMT 16571 12708 0.7668819021181582 1.4252747700600474 chrX 155270560 6367924 0.04101179257677695 0.3665440019533874 chrY 59373566 207825 0.003500295063968366 0.09149302024420548