BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251073.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 1,409,266 number of mapped reads = 466,091 (33.07%) number of supplementary alignments = 18,888 (1.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 233,566 number of mapped paired reads (second in pair) = 232,525 number of mapped paired reads (both in pair) = 455,114 number of mapped paired reads (singletons) = 10,977 number of mapped bases = 55,121,349 bp number of sequenced bases = 55,066,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 249,149 duplication rate = 48.72% >>>>>>> Insert size mean insert size = 95,891.3304 std insert size = 2,873,331.3573 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 52.0776 >>>>>>> ACTG content number of A's = 16,523,944 bp (30.01%) number of C's = 10,959,867 bp (19.9%) number of T's = 16,431,969 bp (29.84%) number of G's = 11,148,233 bp (20.25%) number of N's = 2,015 bp (0%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 458,485 number of insertions = 13,148 mapped reads with insertion percentage = 2.53% number of deletions = 24,769 mapped reads with deletion percentage = 5% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 0.0178X std coverageData = 0.3999X There is a 0.52% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 4488686 0.018008725442653962 0.5272932603354173 chr2 243199373 4870494 0.020026753934106564 0.5775556393712188 chr3 198022430 3672309 0.018544914331169456 0.3344681457742523 chr4 191154276 3474757 0.018177762343124355 0.34792812388364885 chr5 180915260 3322314 0.018363923529723252 0.32925825170392287 chr6 171115067 3098433 0.01810730670490869 0.34388907287504344 chr7 159138663 2883330 0.018118350032889242 0.40746674224213814 chr8 146364022 2754668 0.018820663455121504 0.39235868126071755 chr9 141213431 2273392 0.01609897857378736 0.43627582075411975 chr10 135534747 2673598 0.019726292033437006 0.4697844931277035 chr11 135006516 2458796 0.018212424650673898 0.3592247607804518 chr12 133851895 2591363 0.01935992762747214 0.35799902300476816 chr13 115169878 2099242 0.018227352815290816 0.33344973232405045 chr14 107349540 1841453 0.017153804292035158 0.32843659324685653 chr15 102531392 1699593 0.016576318402075338 0.31661660567554195 chr16 90354753 1444767 0.015989939123623082 0.4174917748062176 chr17 81195210 1243172 0.015310903192442018 0.29956154518029987 chr18 78077248 1556093 0.01993017223148029 0.44043356191291877 chr19 59128983 936583 0.015839660222128293 0.37403717092546673 chr20 63025520 1132027 0.01796140674444257 0.33113206033254183 chr21 48129895 786096 0.016332801058468963 0.32916142240653934 chr22 51304566 552687 0.010772666900641943 0.2595567911505656 chrMT 16571 24122 1.4556755778166677 2.708268018139473 chrX 155270560 3042192 0.019592844902472175 0.3498190893011146 chrY 59373566 201182 0.0033884102565104476 0.23758382590999894