BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084978.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 = 3,478 number of mapped reads = 833 (23.95%) number of supplementary alignments = 11 (0.32%) number of secondary alignments = 0 number of mapped bases = 57,762 bp number of sequenced bases = 57,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1 duplication rate = 0.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.6 >>>>>>> ACTG content number of A's = 17,005 bp (29.46%) number of C's = 10,618 bp (18.4%) number of T's = 17,982 bp (31.15%) number of G's = 12,104 bp (20.97%) number of N's = 11 bp (0.02%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 434 number of insertions = 2 mapped reads with insertion percentage = 0.24% number of deletions = 18 mapped reads with deletion percentage = 2.16% homopolymer indels = 35% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0043X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3422 1.3729153356853622E-5 0.0037595451340187535 chr2 243199373 4276 1.7582282171426485E-5 0.004272741143409697 chr3 198022430 4680 2.3633686345531667E-5 0.004857754618588935 chr4 191154276 4712 2.4650246380049588E-5 0.004963786509116748 chr5 180915260 3482 1.924657986285955E-5 0.0043857901178871814 chr6 171115067 2586 1.5112637626469211E-5 0.003917418891399132 chr7 159138663 3377 2.1220487443708132E-5 0.004606521153171966 chr8 146364022 3081 2.1050255096160175E-5 0.004586518069073246 chr9 141213431 2549 1.8050690943129908E-5 0.004248572126689905 chr10 135534747 2746 2.026048715020658E-5 0.004497019818597064 chr11 135006516 3073 2.276186432364494E-5 0.004765448481758728 chr12 133851895 2590 1.9349744730920694E-5 0.004395393918540201 chr13 115169878 2325 2.0187570225610554E-5 0.004493012651620173 chr14 107349540 1509 1.4056883709049894E-5 0.003749224734937916 chr15 102531392 1909 1.861868802093314E-5 0.0043115058997188135 chr16 90354753 1720 1.9036076607945572E-5 0.004357917619182954 chr17 81195210 1293 1.5924584713802697E-5 0.003990530180490356 chr18 78077248 1703 2.181173188891084E-5 0.004668880900977454 chr19 59128983 1009 1.7064389556640944E-5 0.00413087138062298 chr20 63025520 608 9.646885896379752E-6 0.0031059286588671436 chr21 48129895 618 1.2840252404456731E-5 0.0035833067873648383 chr22 51304566 722 1.4072821510662423E-5 0.003751349552675297 chrMT 16571 0 0.0 0.0 chrX 155270560 3571 2.2998564570128426E-5 0.004795626719851759 chrY 59373566 201 3.3853449193198197E-6 0.001839927568889492