BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238287.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 = 3,102,810 number of mapped reads = 2,779,086 (89.57%) number of supplementary alignments = 22,369 (0.72%) number of secondary alignments = 0 number of mapped bases = 181,632,503 bp number of sequenced bases = 181,544,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,318 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0569 >>>>>>> ACTG content number of A's = 49,676,607 bp (27.36%) number of C's = 34,454,446 bp (18.98%) number of T's = 55,204,542 bp (30.41%) number of G's = 42,164,157 bp (23.23%) number of N's = 44,433 bp (0.02%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,579,211 number of insertions = 15,206 mapped reads with insertion percentage = 0.54% number of deletions = 53,365 mapped reads with deletion percentage = 1.9% homopolymer indels = 44.99% >>>>>>> Coverage mean coverageData = 0.0587X std coverageData = 0.5493X There is a 4.84% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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 14894856 0.059758551213398986 1.0616526891328013 chr2 243199373 13514290 0.055568769907971764 0.7525554045903574 chr3 198022430 10632061 0.05369119548729909 0.27207790652566355 chr4 191154276 13614731 0.07122378470884952 0.35012357856713455 chr5 180915260 11087602 0.06128616237237257 0.29197390449419264 chr6 171115067 14193062 0.08294454865274956 0.5014671408882858 chr7 159138663 10959500 0.06886761389970959 0.7062848879096401 chr8 146364022 8645035 0.059065300897511545 0.6266485300591271 chr9 141213431 5916529 0.041897778122818925 0.5098701240737801 chr10 135534747 9013579 0.0665038242923787 0.5569748255795336 chr11 135006516 8793124 0.06513110819036319 0.4563704202685712 chr12 133851895 9408601 0.07029113035717574 0.31725484538225024 chr13 115169878 4528770 0.03932252146694121 0.2296476093796241 chr14 107349540 3762630 0.035050266633653016 0.26864252966474905 chr15 102531392 4521545 0.044099128196757535 0.25189112774532896 chr16 90354753 4933140 0.05459745985913989 0.32129212942279106 chr17 81195210 2982764 0.03673571384321809 0.2895432734397293 chr18 78077248 5352002 0.06854752360124168 0.8464006883251672 chr19 59128983 3334562 0.05639471255576982 0.6835599205765003 chr20 63025520 4216365 0.06689932903369937 0.31464915988733316 chr21 48129895 1762134 0.03661204746031547 0.26550286284248176 chr22 51304566 2423321 0.04723402201667586 0.2541613861481266 chrMT 16571 7397 0.4463822340232937 0.849803172708556 chrX 155270560 12567161 0.08093717830347234 0.40142986027488237 chrY 59373566 567742 0.009562201468579468 0.22686581282122614