BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230392.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 = 2,583,035 number of mapped reads = 2,076,112 (80.37%) number of supplementary alignments = 10,523 (0.41%) number of secondary alignments = 0 number of mapped bases = 133,251,699 bp number of sequenced bases = 133,189,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,518 duplication rate = 3.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.761 >>>>>>> ACTG content number of A's = 35,554,893 bp (26.7%) number of C's = 22,528,161 bp (16.91%) number of T's = 44,564,647 bp (33.46%) number of G's = 30,293,139 bp (22.74%) number of N's = 248,397 bp (0.19%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,228,978 number of insertions = 12,259 mapped reads with insertion percentage = 0.58% number of deletions = 37,816 mapped reads with deletion percentage = 1.8% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.043X std coverageData = 0.463X There is a 3.75% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% 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 0.01% 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 11234341 0.04507246944833088 0.9130032972711439 chr2 243199373 14660090 0.060280130738659427 0.48187334527025727 chr3 198022430 8198277 0.04140074939995434 0.23063264038900147 chr4 191154276 8906223 0.04659180629576918 0.268426736349898 chr5 180915260 9838457 0.05438157621419 0.2600641165951239 chr6 171115067 6861630 0.040099508011179404 0.293632853492618 chr7 159138663 7034388 0.0442028848765683 0.6246162723810417 chr8 146364022 6221935 0.04251000290221595 0.6983498334696173 chr9 141213431 6745893 0.04777090218847526 0.4871846256618976 chr10 135534747 6394543 0.04718010061287088 0.4859750788316561 chr11 135006516 5136867 0.03804903016681062 0.3289072667532028 chr12 133851895 5906159 0.04412458262171036 0.2435646808063353 chr13 115169878 4264299 0.03702616581741972 0.21136229628982134 chr14 107349540 2928364 0.02727877548427315 0.2177314472426223 chr15 102531392 2994735 0.029207981493121638 0.1887601620523776 chr16 90354753 2929546 0.032422710513081696 0.2506979696600257 chr17 81195210 3364987 0.041443171339787165 0.25395798418392235 chr18 78077248 3132384 0.04011903698245102 0.8132873659874641 chr19 59128983 2011832 0.0340244647874292 0.6429234752773827 chr20 63025520 2689159 0.04266777965497151 0.24385544464786058 chr21 48129895 2120663 0.04406124301746347 0.2585575877959388 chr22 51304566 1461370 0.028484209378167237 0.18501066921648965 chrMT 16571 76247 4.601231066320681 3.2689916332345446 chrX 155270560 7758186 0.04996559553852321 0.30447602842656263 chrY 59373566 381124 0.0064190855573673985 0.16644987951974738