BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240047.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 = 1,931,566 number of mapped reads = 1,589,689 (82.3%) number of supplementary alignments = 10,162 (0.53%) number of secondary alignments = 0 number of mapped bases = 98,749,503 bp number of sequenced bases = 98,701,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,376 duplication rate = 8.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4513 >>>>>>> ACTG content number of A's = 27,129,018 bp (27.49%) number of C's = 17,440,096 bp (17.67%) number of T's = 32,050,982 bp (32.47%) number of G's = 22,016,610 bp (22.31%) number of N's = 64,820 bp (0.07%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 927,739 number of insertions = 7,058 mapped reads with insertion percentage = 0.44% number of deletions = 28,337 mapped reads with deletion percentage = 1.76% homopolymer indels = 48.57% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.3117X There is a 2.21% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 7671741 0.030779225220064748 0.445343120662842 chr2 243199373 10260812 0.042190947589326226 0.38003435856921186 chr3 198022430 6493096 0.03278969963150134 0.24737754880047338 chr4 191154276 6258749 0.03274187285248068 0.25254971897312717 chr5 180915260 5656297 0.03126489716787849 0.243753189184189 chr6 171115067 5641493 0.03296900208092137 0.2839270072024633 chr7 159138663 5923502 0.03722226823031685 0.38353279262060863 chr8 146364022 5401088 0.03690174625018162 0.4680193237574401 chr9 141213431 3541397 0.02507832983677027 0.27686381008575417 chr10 135534747 4413809 0.03256588511579248 0.2862371342486876 chr11 135006516 4373607 0.03239552526486944 0.29741213545310174 chr12 133851895 4706999 0.035165725520733195 0.25639633833308617 chr13 115169878 2517300 0.021857277646851376 0.20189085287934347 chr14 107349540 3581308 0.033361186270569956 0.26044935481434034 chr15 102531392 2336748 0.022790561548213448 0.21227961217870678 chr16 90354753 3200517 0.03542167837036752 0.260047685454293 chr17 81195210 2469097 0.03040939237671779 0.25145514619161935 chr18 78077248 2020934 0.025883776026532083 0.4078775425928661 chr19 59128983 1771643 0.02996234520049161 0.3577630375849649 chr20 63025520 2039320 0.03235705155625848 0.24569758913230788 chr21 48129895 1631030 0.03388808556511499 0.2540974249795769 chr22 51304566 925406 0.01803749787104719 0.1759250380012961 chrMT 16571 42369 2.5568161245549454 2.647048070340206 chrX 155270560 5660814 0.036457741892603465 0.2735897768138961 chrY 59373566 210427 0.003544119280287123 0.08559101124810543