BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237301.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 = 3,166,199 number of mapped reads = 2,814,035 (88.88%) number of supplementary alignments = 33,335 (1.05%) number of secondary alignments = 0 number of mapped bases = 174,826,847 bp number of sequenced bases = 174,742,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,060,665 duplication rate = 21.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.85 >>>>>>> ACTG content number of A's = 44,390,892 bp (25.4%) number of C's = 30,784,790 bp (17.62%) number of T's = 57,762,605 bp (33.06%) number of G's = 41,785,044 bp (23.91%) number of N's = 18,904 bp (0.01%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,032,748 number of insertions = 13,191 mapped reads with insertion percentage = 0.46% number of deletions = 47,984 mapped reads with deletion percentage = 1.69% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.798X There is a 1.69% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 22796584 0.09146049028299111 0.9165966913812024 chr2 243199373 10980178 0.0451488746231266 1.4743079711153686 chr3 198022430 11013159 0.05561571484604042 0.5853674030380381 chr4 191154276 8788304 0.04597492760245656 0.6853083169002915 chr5 180915260 8133765 0.04495897692654561 0.5198344434086765 chr6 171115067 20714211 0.12105427863929714 1.0576884774758786 chr7 159138663 9851016 0.061902091008518775 0.6520059513250149 chr8 146364022 16748763 0.11443224073194709 1.1593363973134945 chr9 141213431 5313691 0.03762879325550839 0.5133325789729182 chr10 135534747 10107059 0.07457171849813539 0.929429226125288 chr11 135006516 5954668 0.044106522977009496 0.5585497231911791 chr12 133851895 1817366 0.013577439452762324 0.27185788888414314 chr13 115169878 7852961 0.06818589318988424 0.6854725097597367 chr14 107349540 4103046 0.03822136545717848 0.47855778680164307 chr15 102531392 3383546 0.033000098155304476 0.4709259509816259 chr16 90354753 4797783 0.053099398102499376 0.5842414701258184 chr17 81195210 4988033 0.061432601750768305 0.6567138199291 chr18 78077248 3264694 0.0418136407676664 1.0511833106805828 chr19 59128983 1616263 0.02733453068184853 0.5567316497937166 chr20 63025520 3837630 0.0608900965830984 0.6334128481741351 chr21 48129895 1618136 0.033620185541647245 0.5386572856307702 chr22 51304566 692680 0.013501332415520288 0.26756541209728424 chrMT 16571 64227 3.875867479331362 5.773302904372859 chrX 155270560 5804181 0.03738107855088563 0.47198302049945806 chrY 59373566 584903 0.00985123581763642 0.44788956134476166