BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084819.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 = 1,979,796 number of mapped reads = 1,787,758 (90.3%) number of supplementary alignments = 18,611 (0.94%) number of secondary alignments = 0 number of mapped bases = 119,301,546 bp number of sequenced bases = 119,254,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,691 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4478 >>>>>>> ACTG content number of A's = 32,393,686 bp (27.16%) number of C's = 22,529,955 bp (18.89%) number of T's = 37,284,127 bp (31.26%) number of G's = 27,030,019 bp (22.67%) number of N's = 16,677 bp (0.01%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 899,627 number of insertions = 9,478 mapped reads with insertion percentage = 0.53% number of deletions = 28,484 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.87% >>>>>>> Coverage mean coverageData = 0.0385X std coverageData = 0.2714X There is a 3.19% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.1% 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% 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 10258431 0.041157093044915626 0.27544975166329266 chr2 243199373 10045601 0.04130603165658655 0.44481749124050995 chr3 198022430 8109773 0.04095381013150884 0.23861260827617978 chr4 191154276 6421062 0.03359099327707427 0.22035446332811676 chr5 180915260 7536021 0.041654977031788255 0.24219982166320464 chr6 171115067 6648445 0.03885365045031365 0.25093504848579 chr7 159138663 7195334 0.04521424187156832 0.27824900888616505 chr8 146364022 7685300 0.052508122522077184 0.2935638170285641 chr9 141213431 7992752 0.05660050848845957 0.32575255815553317 chr10 135534747 3676180 0.02712352427234029 0.20042330202899766 chr11 135006516 5024834 0.03721919614605861 0.26176703065776247 chr12 133851895 4830142 0.03608571996683349 0.2258241760952987 chr13 115169878 2987348 0.025938622597134295 0.19077315654467253 chr14 107349540 2607419 0.024289056105876186 0.18695650509799266 chr15 102531392 3148818 0.03071077002446236 0.21363943915457037 chr16 90354753 2439487 0.026998989195399604 0.20122918195467296 chr17 81195210 3626336 0.04466194495956104 0.25484860990564046 chr18 78077248 4593176 0.058828610352659974 0.4228212556412823 chr19 59128983 2182325 0.03690787308146328 0.2517811174440086 chr20 63025520 2588669 0.04107334616199914 0.2413637866605384 chr21 48129895 885177 0.018391417641779605 0.16567040397954405 chr22 51304566 1259703 0.024553428636351782 0.18393485963664644 chrMT 16571 31552 1.9040492426528273 1.6355444627089726 chrX 155270560 7280048 0.04688620946559348 0.26262366880054094 chrY 59373566 247613 0.004170424932873326 0.09361012767859893