BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080824.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 = 2,151,281 number of mapped reads = 1,850,260 (86.01%) number of supplementary alignments = 18,795 (0.87%) number of secondary alignments = 0 number of mapped bases = 123,518,866 bp number of sequenced bases = 123,474,967 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,666 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6374 >>>>>>> ACTG content number of A's = 33,508,647 bp (27.14%) number of C's = 23,749,813 bp (19.23%) number of T's = 36,758,320 bp (29.77%) number of G's = 29,441,129 bp (23.84%) number of N's = 17,058 bp (0.01%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,135,268 number of insertions = 11,675 mapped reads with insertion percentage = 0.62% number of deletions = 24,951 mapped reads with deletion percentage = 1.33% homopolymer indels = 43.24% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.7284X There is a 3.44% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% 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 0.01% 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 15142719 0.06075298404171278 1.6867001776249135 chr2 243199373 9162080 0.03767312344181085 0.5310449450161396 chr3 198022430 7050038 0.035602219405145165 0.21090605451799588 chr4 191154276 6951094 0.03636379026122335 0.2515638374285117 chr5 180915260 8853766 0.048938746239537784 0.2540129713366 chr6 171115067 8138584 0.04756205366766446 0.4887701551638826 chr7 159138663 8648399 0.05434505252818418 1.141912977212724 chr8 146364022 5619402 0.03839332865558996 1.2804526342111027 chr9 141213431 4380524 0.031020590385626986 0.4693558490937495 chr10 135534747 5374277 0.0396523926074839 0.5715773598851195 chr11 135006516 4995804 0.03700416948764162 0.41127007593877424 chr12 133851895 4794508 0.03581950035148923 0.22522427947573959 chr13 115169878 4513392 0.039188996970197364 0.2193373972724108 chr14 107349540 3254351 0.030315462926063772 0.2588404297260106 chr15 102531392 3073541 0.0299765851223399 0.20265557525495811 chr16 90354753 3191958 0.03532695175427019 0.2910732857039404 chr17 81195210 3432277 0.04227191480876766 0.2954812365950119 chr18 78077248 1953515 0.025020285038734973 1.145771921920087 chr19 59128983 2682060 0.04535948132238297 1.1458643821732013 chr20 63025520 2236456 0.035484927375450455 0.2666111482289381 chr21 48129895 1868115 0.03881402608503509 0.25625882355224944 chr22 51304566 888657 0.0173212068493085 0.14039907194065607 chrMT 16571 45674 2.7562609377828737 2.3198167783530397 chrX 155270560 6854220 0.04414371919570587 0.3113032279510461 chrY 59373566 413455 0.006963620814016797 0.2179608391226302