BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237801.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 = 4,610,540 number of mapped reads = 3,954,178 (85.76%) number of supplementary alignments = 37,860 (0.82%) number of secondary alignments = 0 number of mapped bases = 276,713,056 bp number of sequenced bases = 276,592,566 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 876,190 duplication rate = 17.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6827 >>>>>>> ACTG content number of A's = 81,127,699 bp (29.33%) number of C's = 56,496,206 bp (20.43%) number of T's = 80,189,358 bp (28.99%) number of G's = 58,336,159 bp (21.09%) number of N's = 443,144 bp (0.16%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,411,260 number of insertions = 22,805 mapped reads with insertion percentage = 0.57% number of deletions = 67,380 mapped reads with deletion percentage = 1.68% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0894X std coverageData = 1.6522X There is a 1.22% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 21071277 0.08453851354697327 2.517755517981765 chr2 243199373 14904008 0.06128308562703408 1.4268571291570114 chr3 198022430 26728329 0.1349762701124312 1.792629747850326 chr4 191154276 23619857 0.12356436640737244 1.7210802204022846 chr5 180915260 22668147 0.12529704238326828 1.7099784486264793 chr6 171115067 20285358 0.1185480528140751 1.7751346384111455 chr7 159138663 10837666 0.06810202998877778 1.3258168553294059 chr8 146364022 16140489 0.11027634236506564 1.6776461503360436 chr9 141213431 14284720 0.10115695014874329 1.6446325618282245 chr10 135534747 14566749 0.10747612197188076 1.942918819794044 chr11 135006516 9983513 0.07394837890639293 1.319521402522032 chr12 133851895 11881789 0.08876817918790018 1.4205753484584396 chr13 115169878 3765276 0.032693235986583226 0.8488370548842007 chr14 107349540 5312105 0.04948418968539595 1.0682831530510581 chr15 102531392 7614617 0.07426620132105492 1.2366360278363675 chr16 90354753 4659974 0.05157419886920614 1.1067738089681438 chr17 81195210 11356549 0.1398672286209987 1.9203755849272093 chr18 78077248 3666867 0.04696460356799461 2.2034528040716115 chr19 59128983 6724292 0.11372243625431541 2.0312705154140254 chr20 63025520 6991536 0.11093182571123571 1.6656996644639424 chr21 48129895 2784774 0.057859548623573766 1.1720375348624161 chr22 51304566 3934205 0.076683330680548 1.2980754606930789 chrMT 16571 23952 1.4454166918109952 3.556708912368897 chrX 155270560 12006174 0.07732421393984797 1.288814500416128 chrY 59373566 900833 0.015172290645301649 0.708375265171512