BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234022.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 = 1,145,935 number of mapped reads = 978,915 (85.43%) number of supplementary alignments = 6,076 (0.53%) number of secondary alignments = 0 number of mapped bases = 64,230,714 bp number of sequenced bases = 64,199,209 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,952 duplication rate = 2.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4116 >>>>>>> ACTG content number of A's = 18,082,836 bp (28.17%) number of C's = 11,058,945 bp (17.23%) number of T's = 20,915,725 bp (32.58%) number of G's = 14,129,850 bp (22.01%) number of N's = 11,853 bp (0.02%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 498,473 number of insertions = 4,716 mapped reads with insertion percentage = 0.48% number of deletions = 18,121 mapped reads with deletion percentage = 1.83% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2257X There is a 1.92% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6707480 0.026910584908833586 0.4140195092489456 chr2 243199373 3666700 0.015076930317579396 0.2078212852031589 chr3 198022430 7387764 0.037307713070685984 0.20414907993896644 chr4 191154276 3245162 0.016976664440402054 0.1404736719601747 chr5 180915260 3950508 0.021836234267910842 0.15662966092833408 chr6 171115067 4659201 0.027228467262909117 0.19808162215267378 chr7 159138663 3711341 0.023321428809540773 0.24623505698948803 chr8 146364022 3644850 0.024902636250321134 0.44360219264009887 chr9 141213431 2048611 0.014507196556962063 0.16285078832838276 chr10 135534747 2632198 0.019420835308011457 0.1928745854061597 chr11 135006516 1919562 0.01421829150824098 0.14535489117960138 chr12 133851895 2465263 0.018417841600225384 0.14487443927445767 chr13 115169878 2372369 0.020598867005832897 0.15148467677462873 chr14 107349540 2421158 0.022553967161852765 0.16177198368832457 chr15 102531392 1489504 0.014527297161829229 0.12866661154157202 chr16 90354753 1048742 0.011606937822075614 0.12338091947806289 chr17 81195210 1457245 0.01794742571636923 0.14967838672968684 chr18 78077248 1740865 0.022296700314027463 0.29372331374962923 chr19 59128983 1228503 0.020776663789397493 0.24397027236452495 chr20 63025520 1556085 0.02468976059221725 0.16921528240308054 chr21 48129895 1264712 0.026277057118034436 0.17489274140868347 chr22 51304566 556637 0.010849658098657339 0.10912725064615503 chrMT 16571 23607 1.4245971878583066 1.6098984762174529 chrX 155270560 2880287 0.018550116647998178 0.15022196743655344 chrY 59373566 152360 0.0025661251338684964 0.06565093130660798