BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081922.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 = 2,238,709 number of mapped reads = 2,070,615 (92.49%) number of supplementary alignments = 12,439 (0.56%) number of secondary alignments = 0 number of mapped bases = 141,115,582 bp number of sequenced bases = 141,063,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,346 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4522 >>>>>>> ACTG content number of A's = 39,952,111 bp (28.32%) number of C's = 25,888,752 bp (18.35%) number of T's = 44,855,666 bp (31.8%) number of G's = 30,349,121 bp (21.51%) number of N's = 18,078 bp (0.01%) GC percentage = 39.87% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,072,769 number of insertions = 10,269 mapped reads with insertion percentage = 0.49% number of deletions = 29,643 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.95% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.4345X There is a 3.9% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.07% 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 11840026 0.04750249348425896 0.8303653496142023 chr2 243199373 10031992 0.04125007345310878 0.42496147678828655 chr3 198022430 6837200 0.034527401769587414 0.21340891174179846 chr4 191154276 9048120 0.04733412293638673 0.25866587855710343 chr5 180915260 9227320 0.05100354718557185 0.25461397194326923 chr6 171115067 7206828 0.04211685228162871 0.30088705688881223 chr7 159138663 7569536 0.04756566290870497 0.435942850237387 chr8 146364022 10042080 0.06861030369881473 0.7622146807078207 chr9 141213431 6159567 0.043618846708710024 0.40282628960018724 chr10 135534747 5490234 0.04050794443140105 0.39638954776940327 chr11 135006516 7955735 0.05892852608684458 0.3906265400961509 chr12 133851895 5538195 0.041375544216239894 0.23526532003523404 chr13 115169878 5799980 0.05036021658371471 0.252884486077731 chr14 107349540 4943349 0.04604909345675817 0.2621046752420705 chr15 102531392 4447002 0.04337210207777146 0.2372253061138733 chr16 90354753 3509779 0.03884443134939453 0.2670787034330908 chr17 81195210 3390910 0.0417624389419031 0.26032839031355914 chr18 78077248 2996709 0.0383813348544252 0.8167030556674922 chr19 59128983 2492516 0.042153879088365175 0.599557689755553 chr20 63025520 3203344 0.05082614153758668 0.26490588995125175 chr21 48129895 2130098 0.04425727502625967 0.25912450074783333 chr22 51304566 1532471 0.029870070433886918 0.19291513404000896 chrMT 16571 12529 0.7560798986180677 1.0567331727981442 chrX 155270560 9332179 0.060102694290533894 0.3154129464480566 chrY 59373566 377883 0.00636449897585737 0.13791687475938055