BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084412.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,631,632 number of mapped reads = 1,460,260 (89.5%) number of supplementary alignments = 20,424 (1.25%) number of secondary alignments = 0 number of mapped bases = 97,847,959 bp number of sequenced bases = 97,815,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,980 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3901 >>>>>>> ACTG content number of A's = 27,937,636 bp (28.56%) number of C's = 18,977,678 bp (19.4%) number of T's = 28,820,424 bp (29.46%) number of G's = 21,957,112 bp (22.45%) number of N's = 122,758 bp (0.13%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,010,152 number of insertions = 8,470 mapped reads with insertion percentage = 0.57% number of deletions = 18,766 mapped reads with deletion percentage = 1.27% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.4127X There is a 2.87% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% 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% 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 9569014 0.038391134038538666 0.8889752080574747 chr2 243199373 9193836 0.03780369943634682 0.3686379962887388 chr3 198022430 6353788 0.03208620356794935 0.21020072436336257 chr4 191154276 4687410 0.02452160683028613 0.18418128763003927 chr5 180915260 4921329 0.02720239851519435 0.17703286707680788 chr6 171115067 4624913 0.027028087479871073 0.21397870942075592 chr7 159138663 5683997 0.0357172599847719 0.7158684876950596 chr8 146364022 4668487 0.03189641099094694 0.3356914764805265 chr9 141213431 3625961 0.025677168059177035 0.30118372629924767 chr10 135534747 7083360 0.05226231764759188 0.615742832648649 chr11 135006516 5390409 0.03992702841098425 0.345265652256843 chr12 133851895 4480881 0.03347641062534079 0.19728871459494934 chr13 115169878 2326752 0.020202782536593467 0.148222281231634 chr14 107349540 2635127 0.024547166201177948 0.19335494073861167 chr15 102531392 2150439 0.020973469276609452 0.1595868482580069 chr16 90354753 2223660 0.024610326808153633 0.2204836126631127 chr17 81195210 2814522 0.03466364579881005 0.2420997149929629 chr18 78077248 2582045 0.033070389468645205 0.6090381358779534 chr19 59128983 2353882 0.039809275934950546 0.582213064609901 chr20 63025520 1994461 0.03164529225621621 0.19901002694653316 chr21 48129895 999913 0.020775299842229034 0.17303778155039576 chr22 51304566 854504 0.01665551561239208 0.13501909345018315 chrMT 16571 45233 2.729648180556394 2.275760889247349 chrX 155270560 6318013 0.040690347223581856 0.27152843272232347 chrY 59373566 266023 0.004480495579463764 0.11518901971314845