BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068081.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 = 1,995,449 number of mapped reads = 1,804,931 (90.45%) number of supplementary alignments = 16,607 (0.83%) number of secondary alignments = 0 number of mapped bases = 121,078,986 bp number of sequenced bases = 121,026,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,172 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5064 >>>>>>> ACTG content number of A's = 33,808,653 bp (27.93%) number of C's = 22,190,414 bp (18.34%) number of T's = 38,624,256 bp (31.91%) number of G's = 26,400,687 bp (21.81%) number of N's = 2,755 bp (0%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 925,553 number of insertions = 9,945 mapped reads with insertion percentage = 0.55% number of deletions = 32,011 mapped reads with deletion percentage = 1.75% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.4263X There is a 3.16% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 13954782 0.055986949777750004 0.8590858708097222 chr2 243199373 12167340 0.05003030990544536 0.44370409087578117 chr3 198022430 9474362 0.04784489312650087 0.25919878463649976 chr4 191154276 6481643 0.03390791530083272 0.22994016391477398 chr5 180915260 5048196 0.02790364947655604 0.19984701157395846 chr6 171115067 8561471 0.05003341406516821 0.29368253794916527 chr7 159138663 8090756 0.05084091978327102 0.489710710925338 chr8 146364022 4144872 0.028318926628020647 0.851499629256126 chr9 141213431 5527528 0.0391430755619839 0.3664474622030201 chr10 135534747 5164147 0.0381020152714049 0.31107149436935433 chr11 135006516 6448953 0.047767716633766034 0.3503963571996313 chr12 133851895 5888589 0.043993318137184385 0.2574687813619426 chr13 115169878 2852652 0.024769080679238022 0.1888745190633815 chr14 107349540 1926631 0.017947268334824722 0.18508315433023792 chr15 102531392 1307846 0.012755566607346948 0.14218356329741938 chr16 90354753 2730223 0.030216705921380805 0.22410297605084778 chr17 81195210 3547188 0.043687158392717994 0.282614646122803 chr18 78077248 3898994 0.04993764636786378 0.5537367802589604 chr19 59128983 2324338 0.03930962249088573 0.5713417106059411 chr20 63025520 2044519 0.03243954195062571 0.22975190272064894 chr21 48129895 2284227 0.047459629820509684 0.26710313293725046 chr22 51304566 1043241 0.02033427200222296 0.16503903705917974 chrMT 16571 12887 0.7776839056182487 1.1603277902899143 chrX 155270560 5849018 0.0376698454620116 0.2525018577024397 chrY 59373566 304583 0.0051299428435880035 0.1117508062861694