BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238599.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 = 3,806,221 number of mapped reads = 3,367,760 (88.48%) number of supplementary alignments = 33,861 (0.89%) number of secondary alignments = 0 number of mapped bases = 206,336,857 bp number of sequenced bases = 206,232,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 870,947 duplication rate = 18.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6277 >>>>>>> ACTG content number of A's = 51,298,743 bp (24.87%) number of C's = 37,428,646 bp (18.15%) number of T's = 67,644,777 bp (32.8%) number of G's = 49,850,035 bp (24.17%) number of N's = 10,496 bp (0.01%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,190,810 number of insertions = 11,656 mapped reads with insertion percentage = 0.34% number of deletions = 60,945 mapped reads with deletion percentage = 1.79% homopolymer indels = 40.6% >>>>>>> Coverage mean coverageData = 0.0667X std coverageData = 0.973X There is a 3.25% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 13729167 0.055081776506386314 1.1958573484163089 chr2 243199373 23615395 0.09710302583715955 2.5124419879579154 chr3 198022430 4680263 0.023635014477905357 0.29696739976724806 chr4 191154276 12965471 0.06782726115946264 0.4781323637892082 chr5 180915260 14203446 0.0785088333620945 0.5151896064825299 chr6 171115067 21004778 0.122752358212851 1.113952660503398 chr7 159138663 7298177 0.04586048960333417 0.5040505853338404 chr8 146364022 12738960 0.08703614334949063 0.8024513697207772 chr9 141213431 5063101 0.03585424533732914 0.4601786635211084 chr10 135534747 18988902 0.14010357063639187 0.7110609557356601 chr11 135006516 15945211 0.11810697344415584 0.7129276960769455 chr12 133851895 7309949 0.05461221897530849 0.4489111386139256 chr13 115169878 3141518 0.027277253866675105 0.5086047752951603 chr14 107349540 4494046 0.041863672634274915 0.4125576654553584 chr15 102531392 4105385 0.04004027371441519 0.6955815639822132 chr16 90354753 3351077 0.03708799912274676 0.40277381187576217 chr17 81195210 6976382 0.08592110298132119 0.5637076924830594 chr18 78077248 3073873 0.039369638130688216 1.3425777272753587 chr19 59128983 5755902 0.09734485032492442 0.8347284177980422 chr20 63025520 5066999 0.08039598879945774 0.5370739895011933 chr21 48129895 3719742 0.07728547922242507 0.5272821321996637 chr22 51304566 1165944 0.02272593047566176 0.27001033526646706 chrMT 16571 53919 3.253816909057993 3.2112443181096606 chrX 155270560 7486653 0.04821682230037684 0.4094153627222639 chrY 59373566 402597 0.0067807448183253806 0.2503673425906721