BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237608.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 = 1,478,962 number of mapped reads = 1,305,436 (88.27%) number of supplementary alignments = 6,085 (0.41%) number of secondary alignments = 0 number of mapped bases = 83,257,620 bp number of sequenced bases = 83,204,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,264 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6087 >>>>>>> ACTG content number of A's = 22,241,761 bp (26.73%) number of C's = 14,224,576 bp (17.1%) number of T's = 27,435,834 bp (32.97%) number of G's = 19,158,441 bp (23.03%) number of N's = 144,242 bp (0.17%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 743,689 number of insertions = 7,071 mapped reads with insertion percentage = 0.54% number of deletions = 31,729 mapped reads with deletion percentage = 2.4% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.2641X There is a 2.4% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7406966 0.029716941006136952 0.3912393671285177 chr2 243199373 8186565 0.03366194944918711 0.47029981527643494 chr3 198022430 5589719 0.028227706325995496 0.18457631247353348 chr4 191154276 3278718 0.017152208512458283 0.1546156216660593 chr5 180915260 5722668 0.03163175953205937 0.19604903846560237 chr6 171115067 4070038 0.0237853864733022 0.2311814828214287 chr7 159138663 4922042 0.030929265756116098 0.29721662138261024 chr8 146364022 3987550 0.02724405865261068 0.3399263866127815 chr9 141213431 3219937 0.02280191747483283 0.20334274702336338 chr10 135534747 4493405 0.03315315887224108 0.2518918994779089 chr11 135006516 2445575 0.01811449604402798 0.16449921765852726 chr12 133851895 3657780 0.027327069220798108 0.18259417986535703 chr13 115169878 3688170 0.03202373801246885 0.20240853104109177 chr14 107349540 2806243 0.02614117396311153 0.18324586274217228 chr15 102531392 1351230 0.01317869555501597 0.13031470407469126 chr16 90354753 1836250 0.020322671901941893 0.18197470576355917 chr17 81195210 1629335 0.020066885718997462 0.15862109913264688 chr18 78077248 1411944 0.01808393656497729 0.2880607965206063 chr19 59128983 1586123 0.026824797578541136 0.2931459801896771 chr20 63025520 1451414 0.023028988892118622 0.17261860806706567 chr21 48129895 1536356 0.03192103369433904 0.20109112472239163 chr22 51304566 521469 0.010164183047567344 0.10845715483862829 chrMT 16571 5020 0.30293886910868384 0.6301061708627482 chrX 155270560 8186826 0.052726196131449514 0.26804585262478886 chrY 59373566 266277 0.004484773577521014 0.10082286432388587