BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238623.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 = 4,622,081 number of mapped reads = 4,223,583 (91.38%) number of supplementary alignments = 33,263 (0.72%) number of secondary alignments = 0 number of mapped bases = 260,120,886 bp number of sequenced bases = 260,013,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 316,548 duplication rate = 5.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.025 >>>>>>> ACTG content number of A's = 64,284,038 bp (24.72%) number of C's = 47,488,761 bp (18.26%) number of T's = 83,699,371 bp (32.19%) number of G's = 64,528,201 bp (24.82%) number of N's = 12,829 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,413,039 number of insertions = 18,842 mapped reads with insertion percentage = 0.44% number of deletions = 61,266 mapped reads with deletion percentage = 1.44% homopolymer indels = 41.79% >>>>>>> Coverage mean coverageData = 0.084X std coverageData = 0.8404X There is a 6.76% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 22746504 0.09125956801527889 1.1729784146745212 chr2 243199373 23103909 0.09499987074391018 1.7756589268473533 chr3 198022430 19173224 0.09682349620697009 0.3890329825465794 chr4 191154276 11466383 0.05998496732555436 0.3314824710095372 chr5 180915260 14471687 0.07999152199764685 0.3555148372963151 chr6 171115067 21698593 0.1268070274606502 0.8350992232994501 chr7 159138663 14877394 0.09348698625173192 1.3723643028612016 chr8 146364022 16707583 0.11415088743598478 0.7654256820189954 chr9 141213431 8662375 0.061342429956255363 0.6802363122563639 chr10 135534747 15822391 0.11674047689040214 0.6268140862482401 chr11 135006516 7749099 0.057397962924989485 0.404687230262388 chr12 133851895 8739564 0.06529279245542247 0.35990244127628235 chr13 115169878 6040326 0.05244709905831454 0.3908615640911671 chr14 107349540 6467440 0.060246555318262195 0.4232349602729225 chr15 102531392 5142892 0.050159194171478724 0.4125463651455344 chr16 90354753 7558488 0.08365346314432402 0.48814095373088784 chr17 81195210 5993142 0.0738115216402544 0.3410432173714382 chr18 78077248 10477632 0.13419571345547426 1.39149022203244 chr19 59128983 4694554 0.0793951419729306 0.8002008931390143 chr20 63025520 7398173 0.11738376771821954 0.46533763987183263 chr21 48129895 4875590 0.10130065731495987 0.4459777011128863 chr22 51304566 2189258 0.04267179650247894 0.2487521730277811 chrMT 16571 222693 13.438718242713174 9.604396062659387 chrX 155270560 13222906 0.08516041933512702 0.42738840870262496 chrY 59373566 619086 0.010426963406577264 0.27191230241472886