BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237283.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 = 2,094,327 number of mapped reads = 1,841,261 (87.92%) number of supplementary alignments = 19,578 (0.93%) number of secondary alignments = 0 number of mapped bases = 113,740,262 bp number of sequenced bases = 113,672,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 478,708 duplication rate = 19.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0372 >>>>>>> ACTG content number of A's = 29,217,804 bp (25.7%) number of C's = 19,005,439 bp (16.72%) number of T's = 38,737,854 bp (34.08%) number of G's = 26,700,287 bp (23.49%) number of N's = 11,452 bp (0.01%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 732,454 number of insertions = 8,770 mapped reads with insertion percentage = 0.47% number of deletions = 38,956 mapped reads with deletion percentage = 2.09% homopolymer indels = 41.73% >>>>>>> Coverage mean coverageData = 0.0367X std coverageData = 0.5892X There is a 1.87% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 8398466 0.033694864896645534 0.7407787476348688 chr2 243199373 9685782 0.03982650892771833 1.2318673101948183 chr3 198022430 12463450 0.06293958719726851 0.436446836652539 chr4 191154276 5626161 0.029432566813205895 0.39195044412011304 chr5 180915260 7852660 0.04340518317802489 0.36081793077636554 chr6 171115067 15575646 0.09102439821970791 0.8501762447914367 chr7 159138663 7162615 0.04500864130044878 0.4763111802010893 chr8 146364022 6782155 0.0463375828794866 0.7925180256827855 chr9 141213431 4271991 0.030252016183928 0.34336372472347154 chr10 135534747 6380242 0.04707458523532714 0.5750677983882201 chr11 135006516 2666329 0.019749631936283728 0.24587351384770256 chr12 133851895 2139257 0.015982269059395836 0.22410567561336506 chr13 115169878 4931604 0.042820258956947056 0.3948854655022241 chr14 107349540 1631788 0.015200698577748913 0.21893739757327113 chr15 102531392 2327108 0.02269654156260748 0.28389522414336515 chr16 90354753 1655432 0.018321471146072417 0.25385806145082096 chr17 81195210 2137559 0.02632617121133131 0.2949057027870932 chr18 78077248 1929012 0.024706454817669803 0.8894178839247011 chr19 59128983 1300686 0.02199743567380484 0.42666494334525107 chr20 63025520 1636475 0.025965275653417854 0.28919904393622026 chr21 48129895 1761677 0.03660255232221055 0.3700218572610912 chr22 51304566 772020 0.01504778346629031 0.20089359088339173 chrMT 16571 6207 0.3745700319835858 0.9009139872566025 chrX 155270560 4305111 0.0277265117096248 0.28970170356849795 chrY 59373566 340829 0.005740416534859975 0.29596639474936826