BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240017.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 = 1,558,544 number of mapped reads = 1,221,393 (78.37%) number of supplementary alignments = 3,720 (0.24%) number of secondary alignments = 0 number of mapped bases = 72,627,611 bp number of sequenced bases = 72,583,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,075 duplication rate = 8.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7557 >>>>>>> ACTG content number of A's = 19,453,307 bp (26.8%) number of C's = 11,814,722 bp (16.28%) number of T's = 23,828,854 bp (32.83%) number of G's = 17,440,272 bp (24.03%) number of N's = 46,807 bp (0.06%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 763,021 number of insertions = 5,386 mapped reads with insertion percentage = 0.44% number of deletions = 25,653 mapped reads with deletion percentage = 2.07% homopolymer indels = 51.21% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.2678X There is a 1.76% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.04% 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 4877542 0.01956882586864247 0.2689223576762772 chr2 243199373 8311933 0.03417744419924964 0.3338747750370652 chr3 198022430 5182410 0.02617082317392025 0.2271960960629563 chr4 191154276 5336707 0.027918323940605963 0.23477319037663485 chr5 180915260 3944355 0.021802223869893562 0.20053497503332615 chr6 171115067 3984227 0.02328390520982001 0.22648567415874946 chr7 159138663 4123087 0.025908769888308036 0.5514908815575056 chr8 146364022 4689110 0.03203731310417256 0.3426091613377966 chr9 141213431 2424962 0.01717231840362267 0.22493016497113907 chr10 135534747 2964752 0.02187447916953724 0.21243894932890253 chr11 135006516 3610474 0.026742961058264774 0.2755098764803558 chr12 133851895 3426948 0.025602536295806645 0.20871957154649004 chr13 115169878 1644546 0.014279306608278251 0.16283357180912886 chr14 107349540 2681228 0.024976613779621227 0.21329038231936084 chr15 102531392 1822435 0.017774410007034724 0.20085483469819504 chr16 90354753 1649476 0.018255553197074205 0.1774294271745835 chr17 81195210 1963933 0.024187793836606863 0.22214902733726014 chr18 78077248 1665705 0.021334063926023623 0.3217708556818974 chr19 59128983 1150432 0.019456312989519876 0.23228406030973922 chr20 63025520 1313264 0.020837019670761937 0.20176262314074347 chr21 48129895 1027357 0.021345506779102675 0.19987130867953984 chr22 51304566 659595 0.012856458039231829 0.14531908549018424 chrMT 16571 60121 3.6280852091002354 4.971902898743966 chrX 155270560 3953570 0.02546245727457929 0.23316384157260978 chrY 59373566 159442 0.002685403804110402 0.068286965807397