BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432721.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 398,969,730 number of mapped reads = 398,809,161 (99.96%) number of supplementary alignments = 5,153,462 (1.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 199,408,831 number of mapped paired reads (second in pair) = 199,400,330 number of mapped paired reads (both in pair) = 398,748,002 number of mapped paired reads (singletons) = 61,159 number of mapped bases = 55,444,091,379 bp number of sequenced bases = 55,387,471,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 199,410,197 duplication rate = 32.87% >>>>>>> Insert size mean insert size = 63,150.2672 std insert size = 2,540,178.6951 median insert size = 318 >>>>>>> Mapping quality mean mapping quality = 57.3957 >>>>>>> ACTG content number of A's = 15,451,231,573 bp (27.9%) number of C's = 11,732,161,882 bp (21.18%) number of T's = 15,250,560,581 bp (27.53%) number of G's = 12,942,994,346 bp (23.37%) number of N's = 10,522,890 bp (0.02%) GC percentage = 44.55% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 438,482,752 number of insertions = 12,269,677 mapped reads with insertion percentage = 3.01% number of deletions = 39,399,227 mapped reads with deletion percentage = 9.4% homopolymer indels = 53.06% >>>>>>> Coverage mean coverageData = 17.9101X std coverageData = 51.8984X There is a 53.11% of reference with a coverageData >= 1X There is a 46.8% of reference with a coverageData >= 2X There is a 42.54% of reference with a coverageData >= 3X There is a 39.33% of reference with a coverageData >= 4X There is a 36.7% of reference with a coverageData >= 5X There is a 34.47% of reference with a coverageData >= 6X There is a 32.55% of reference with a coverageData >= 7X There is a 30.86% of reference with a coverageData >= 8X There is a 29.37% of reference with a coverageData >= 9X There is a 28.03% of reference with a coverageData >= 10X There is a 26.81% of reference with a coverageData >= 11X There is a 25.71% of reference with a coverageData >= 12X There is a 24.7% of reference with a coverageData >= 13X There is a 23.77% of reference with a coverageData >= 14X There is a 22.91% of reference with a coverageData >= 15X There is a 22.11% of reference with a coverageData >= 16X There is a 21.37% of reference with a coverageData >= 17X There is a 20.67% of reference with a coverageData >= 18X There is a 20.02% of reference with a coverageData >= 19X There is a 19.4% of reference with a coverageData >= 20X There is a 18.82% of reference with a coverageData >= 21X There is a 18.28% of reference with a coverageData >= 22X There is a 17.76% of reference with a coverageData >= 23X There is a 17.26% of reference with a coverageData >= 24X There is a 16.8% of reference with a coverageData >= 25X There is a 16.35% of reference with a coverageData >= 26X There is a 15.92% of reference with a coverageData >= 27X There is a 15.52% of reference with a coverageData >= 28X There is a 15.13% of reference with a coverageData >= 29X There is a 14.75% of reference with a coverageData >= 30X There is a 14.4% of reference with a coverageData >= 31X There is a 14.05% of reference with a coverageData >= 32X There is a 13.73% of reference with a coverageData >= 33X There is a 13.41% of reference with a coverageData >= 34X There is a 13.1% of reference with a coverageData >= 35X There is a 12.81% of reference with a coverageData >= 36X There is a 12.53% of reference with a coverageData >= 37X There is a 12.26% of reference with a coverageData >= 38X There is a 12% of reference with a coverageData >= 39X There is a 11.75% of reference with a coverageData >= 40X There is a 11.5% of reference with a coverageData >= 41X There is a 11.27% of reference with a coverageData >= 42X There is a 11.04% of reference with a coverageData >= 43X There is a 10.82% of reference with a coverageData >= 44X There is a 10.6% of reference with a coverageData >= 45X There is a 10.4% of reference with a coverageData >= 46X There is a 10.2% of reference with a coverageData >= 47X There is a 10% of reference with a coverageData >= 48X There is a 9.81% of reference with a coverageData >= 49X There is a 9.63% of reference with a coverageData >= 50X There is a 9.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5008565234 20.09449450479002 56.11092758428481 chr2 243199373 4375186260 17.99012146301874 54.08121010818342 chr3 198022430 4533424911 22.893491969571325 60.26242253967464 chr4 191154276 2559331094 13.388824710361174 39.65851570145075 chr5 180915260 3307311799 18.280999618274322 51.09290950050604 chr6 171115067 3259697197 19.049738016348964 52.45545255860695 chr7 159138663 3065790807 19.264902376363437 53.45748087033562 chr8 146364022 2179308819 14.889648352243286 41.619953718489214 chr9 141213431 2212781317 15.669765271831686 47.05840381936741 chr10 135534747 3181251113 23.4718489790666 60.41923724101639 chr11 135006516 2988474456 22.13577940193642 57.589377541194 chr12 133851895 2399636969 17.927553203486585 50.35059705140344 chr13 115169878 1634219951 14.189647322540361 43.68437623780895 chr14 107349540 1357116371 12.64203247633851 38.674524022473896 chr15 102531392 1291262357 12.593824504011415 39.48715848286019 chr16 90354753 2450399373 27.119761735168485 75.8462945445179 chr17 81195210 2218031177 27.317266338740918 69.45212013750388 chr18 78077248 1587978530 20.338556630479598 56.54784232212365 chr19 59128983 1163992676 19.68565358210203 55.43730397843127 chr20 63025520 1183172006 18.77290351590911 49.38407024490261 chr21 48129895 783341714 16.27557496229734 52.3466679843434 chr22 51304566 902563652 17.5922675576283 52.82678488974425 chrMT 16571 5199138 313.74920041035546 481.4545499251916 chrX 155270560 1705934372 10.986850127931527 33.53619460084896 chrY 59373566 90120086 1.5178486331779364 17.853763162414925