BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240265.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 = 1,602,591 number of mapped reads = 1,214,699 (75.8%) number of supplementary alignments = 4,257 (0.27%) number of secondary alignments = 0 number of mapped bases = 70,235,174 bp number of sequenced bases = 70,191,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,665 duplication rate = 9.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5079 >>>>>>> ACTG content number of A's = 18,601,451 bp (26.5%) number of C's = 11,059,249 bp (15.76%) number of T's = 23,325,728 bp (33.23%) number of G's = 17,190,744 bp (24.49%) number of N's = 14,566 bp (0.02%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 735,155 number of insertions = 4,929 mapped reads with insertion percentage = 0.4% number of deletions = 26,166 mapped reads with deletion percentage = 2.13% homopolymer indels = 50.75% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.2764X There is a 1.6% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.06% 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% 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 4929224 0.01977617540218686 0.2685474920044221 chr2 243199373 7729920 0.03178429247019481 0.33244655287429914 chr3 198022430 5459205 0.02756861937306799 0.24876304342705172 chr4 191154276 5709133 0.02986662458965867 0.25873374903368107 chr5 180915260 3635172 0.020093230388636096 0.20514614011555804 chr6 171115067 3924257 0.0229334392862085 0.23723218149721803 chr7 159138663 4254511 0.026734615710576882 0.6297877627196269 chr8 146364022 4277099 0.02922233853344096 0.2884984164167804 chr9 141213431 2496679 0.01768018086041688 0.2284363290784761 chr10 135534747 2512123 0.018534900131550767 0.20296119928731482 chr11 135006516 3171673 0.02349274015781579 0.24693379913236177 chr12 133851895 2834943 0.021179700145448073 0.20714336721932958 chr13 115169878 1781325 0.015466934852531493 0.17892325253726038 chr14 107349540 2316457 0.021578639275026238 0.2186279431929065 chr15 102531392 1879685 0.01833277558545192 0.2133174012224921 chr16 90354753 1563859 0.017307988213968114 0.1831046592728584 chr17 81195210 1948067 0.023992388220930767 0.22683168783716803 chr18 78077248 1548965 0.01983887803012729 0.2846933053567593 chr19 59128983 1071543 0.018122128026453625 0.224793218953982 chr20 63025520 1304870 0.020703835525672776 0.21137936407610172 chr21 48129895 978617 0.020332830561961543 0.20711875613115074 chr22 51304566 588613 0.01147291646517388 0.14695770327027532 chrMT 16571 75427 4.551747027940378 6.398281935091732 chrX 155270560 4087027 0.026321969857003157 0.25076249307820503 chrY 59373566 156780 0.0026405690370694596 0.06861827536445991