BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013314.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 = 2,529,761 number of mapped reads = 2,292,681 (90.63%) number of supplementary alignments = 11,611 (0.46%) number of secondary alignments = 0 number of mapped bases = 150,912,418 bp number of sequenced bases = 150,851,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,218 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2337 >>>>>>> ACTG content number of A's = 41,269,423 bp (27.36%) number of C's = 28,726,435 bp (19.04%) number of T's = 46,235,284 bp (30.65%) number of G's = 34,583,420 bp (22.93%) number of N's = 37,237 bp (0.02%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,138,404 number of insertions = 10,498 mapped reads with insertion percentage = 0.45% number of deletions = 34,497 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.3703X There is a 4.13% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 11027656 0.044243243831276154 0.4647079718869911 chr2 243199373 15589772 0.06410284618620296 0.5114489043554475 chr3 198022430 9400440 0.04747159198076703 0.24889634043547462 chr4 191154276 9474732 0.049565890956056874 0.26675368651003195 chr5 180915260 8121477 0.044891055624605686 0.24295852952836064 chr6 171115067 8120806 0.04745815866699804 0.2972687849286517 chr7 159138663 9255447 0.05815963779964646 0.6374451814725353 chr8 146364022 8427240 0.057577264445493305 0.4526914475589754 chr9 141213431 5386103 0.03814157734047267 0.3007822274253265 chr10 135534747 7021927 0.05180905380669652 0.3684914851638583 chr11 135006516 6274360 0.04647449757165795 0.2994866297323751 chr12 133851895 7389772 0.05520857213116034 0.2743048570675561 chr13 115169878 3698514 0.032113553163614535 0.21605550433686105 chr14 107349540 4976602 0.04635885724335661 0.2625475837170107 chr15 102531392 4249012 0.041441083721949275 0.24559250933069698 chr16 90354753 4891242 0.05413375431395402 0.2850764078676498 chr17 81195210 4118987 0.05072943342347412 0.2830813764775882 chr18 78077248 3653994 0.04679972839206628 0.5143720089828261 chr19 59128983 3153503 0.053332610168519215 0.4088229126359986 chr20 63025520 3540117 0.056169580195450985 0.2766172916619627 chr21 48129895 2550187 0.052985509318065206 0.2780364364724818 chr22 51304566 1549613 0.030204192741831205 0.19727185478601492 chrMT 16571 395499 23.8669362138676 25.330819982320826 chrX 155270560 8289527 0.053387628665730325 0.27998219074753 chrY 59373566 355889 0.0059940647661284145 0.1289374006127868