BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004137.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 = 1,741,263 number of mapped reads = 1,548,965 (88.96%) number of supplementary alignments = 14,406 (0.83%) number of secondary alignments = 0 number of mapped bases = 100,814,234 bp number of sequenced bases = 100,765,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,466 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9503 >>>>>>> ACTG content number of A's = 27,843,328 bp (27.63%) number of C's = 18,642,841 bp (18.5%) number of T's = 30,428,991 bp (30.2%) number of G's = 23,830,149 bp (23.65%) number of N's = 20,438 bp (0.02%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 901,373 number of insertions = 9,249 mapped reads with insertion percentage = 0.59% number of deletions = 28,966 mapped reads with deletion percentage = 1.85% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.3589X There is a 2.97% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 7920860 0.0317786971531758 0.740662077500043 chr2 243199373 8036451 0.033044702792058595 0.4042076221713515 chr3 198022430 6808090 0.03438039822054502 0.20163153182868804 chr4 191154276 5708036 0.029860885769565523 0.1996366099256206 chr5 180915260 5656546 0.03126627350285432 0.19013709974522933 chr6 171115067 5784709 0.03380595935482408 0.2212912111016031 chr7 159138663 5943335 0.037346895392730554 0.4656120750856291 chr8 146364022 6998424 0.04781519327201872 0.3838361859343219 chr9 141213431 3342118 0.02366713970712885 0.3016573405982533 chr10 135534747 5389390 0.03976389906862777 0.3945452366059635 chr11 135006516 4440867 0.03289372344072637 0.29641295498256837 chr12 133851895 4934357 0.036864304386575925 0.2086602769306555 chr13 115169878 2938814 0.02551721032473439 0.16882689130685594 chr14 107349540 2457445 0.02289199376168729 0.19120544050162644 chr15 102531392 2414758 0.023551401701441838 0.17246303478369895 chr16 90354753 2668035 0.02952844107713957 0.23239944570460655 chr17 81195210 2781852 0.034261282161841815 0.22110412936124393 chr18 78077248 2714043 0.03476099721137712 0.6359011311565326 chr19 59128983 2041733 0.0345301558797316 0.5017708581344882 chr20 63025520 2229172 0.03536935514375764 0.21708805884247875 chr21 48129895 1333640 0.027709181580387824 0.19825882040187304 chr22 51304566 1265559 0.024667570523839926 0.16525480727860414 chrMT 16571 104936 6.332508599360328 4.778941058527601 chrX 155270560 6601079 0.04251339725959641 0.256826455008109 chrY 59373566 299985 0.005052500973244558 0.1096633077269879