BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231858.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 = 840,668 number of mapped reads = 632,757 (75.27%) number of supplementary alignments = 2,615 (0.31%) number of secondary alignments = 0 number of mapped bases = 39,299,661 bp number of sequenced bases = 39,277,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,831 duplication rate = 6.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2025 >>>>>>> ACTG content number of A's = 10,298,300 bp (26.22%) number of C's = 6,539,665 bp (16.65%) number of T's = 12,940,038 bp (32.95%) number of G's = 9,497,612 bp (24.18%) number of N's = 1,751 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 323,947 number of insertions = 3,163 mapped reads with insertion percentage = 0.5% number of deletions = 12,607 mapped reads with deletion percentage = 1.97% homopolymer indels = 50.08% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1506X There is a 1.02% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 3382716 0.013571544923051565 0.1508548425015024 chr2 243199373 3481036 0.014313507296747841 0.18137731907761614 chr3 198022430 2842089 0.014352358972667895 0.14750205710369482 chr4 191154276 2366735 0.012381282017463214 0.14502499759175422 chr5 180915260 2093346 0.011570864724180813 0.13066586266368954 chr6 171115067 2491581 0.014560851032480967 0.1509520230833777 chr7 159138663 2256952 0.014182298364540111 0.19168544917345126 chr8 146364022 2131819 0.01456518460527137 0.19165570661069498 chr9 141213431 1569867 0.011116980792004126 0.13761084756537564 chr10 135534747 1777672 0.013115987149774957 0.1415625184355921 chr11 135006516 1876762 0.013901269772786374 0.1743550451597037 chr12 133851895 1830218 0.013673456023913596 0.1435034758094792 chr13 115169878 1210547 0.010510968848990184 0.1258824914110946 chr14 107349540 1303315 0.012140853141988312 0.13476972894093883 chr15 102531392 1241318 0.01210671166933928 0.13788742439570198 chr16 90354753 1044361 0.011558451164157352 0.13077696071452133 chr17 81195210 1053472 0.012974558474570113 0.14766235098265765 chr18 78077248 1116626 0.014301554276093338 0.16785284148628624 chr19 59128983 783198 0.013245585502459935 0.1433980461842611 chr20 63025520 889004 0.014105460772080896 0.1484715181869588 chr21 48129895 531708 0.01104735424833152 0.12871721934303057 chr22 51304566 451810 0.00880642865198392 0.11512281694391917 chrMT 16571 8182 0.4937541488141935 0.9301888283956118 chrX 155270560 1328788 0.008557887599555255 0.1157779640915832 chrY 59373566 236539 0.003983910954582044 0.0765961226668146