BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238666.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 = 2,300,199 number of mapped reads = 1,840,335 (80.01%) number of supplementary alignments = 12,402 (0.54%) number of secondary alignments = 0 number of mapped bases = 113,741,380 bp number of sequenced bases = 113,690,660 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 258,019 duplication rate = 11.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2661 >>>>>>> ACTG content number of A's = 27,571,242 bp (24.25%) number of C's = 20,309,151 bp (17.86%) number of T's = 37,798,062 bp (33.25%) number of G's = 28,006,437 bp (24.63%) number of N's = 5,768 bp (0.01%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 635,275 number of insertions = 7,830 mapped reads with insertion percentage = 0.42% number of deletions = 29,516 mapped reads with deletion percentage = 1.59% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0367X std coverageData = 0.452X There is a 2.67% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11382695 0.04566766957021945 0.554065732253472 chr2 243199373 8499390 0.034948239771983296 1.0353130458384865 chr3 198022430 7171058 0.03621336229436231 0.25723677363127606 chr4 191154276 6537818 0.03420178787944037 0.25310904646156535 chr5 180915260 6186357 0.034194777156996044 0.2463822915853833 chr6 171115067 6264827 0.036611778903140074 0.4179023472846607 chr7 159138663 6715167 0.04219695499138384 0.5043688073978793 chr8 146364022 5636504 0.038510174310459985 0.3219695655128611 chr9 141213431 4591796 0.032516708697489266 0.2921260524680261 chr10 135534747 5634626 0.041573294854049495 0.3352105570450711 chr11 135006516 5171890 0.038308447275241145 0.2993409638728682 chr12 133851895 4810298 0.03593746655585264 0.2552460576436582 chr13 115169878 3371745 0.02927627482595753 0.29201919494081374 chr14 107349540 3728936 0.03473639477169627 0.2537568991213165 chr15 102531392 3283530 0.032024631051532006 0.3135491253060137 chr16 90354753 3184633 0.03524588241639043 0.27713334976809917 chr17 81195210 4153416 0.05115346089997181 0.3103162568240268 chr18 78077248 3052045 0.03909006885078736 0.7001482950653012 chr19 59128983 2615494 0.044233705152682906 0.4157297565870386 chr20 63025520 2331281 0.03698947664374685 0.2624718738418432 chr21 48129895 1438086 0.029879267345170813 0.2462868828226353 chr22 51304566 1567863 0.030559911568104874 0.2292291902159271 chrMT 16571 389511 23.505582040914852 14.208044281431361 chrX 155270560 5710371 0.03677690735449141 0.2646450084222233 chrY 59373566 312043 0.0052555879833796745 0.17377931559541415