BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068123.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 = 3,416,228 number of mapped reads = 3,134,303 (91.75%) number of supplementary alignments = 20,118 (0.59%) number of secondary alignments = 0 number of mapped bases = 193,270,789 bp number of sequenced bases = 193,178,096 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 889,877 duplication rate = 20.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7146 >>>>>>> ACTG content number of A's = 49,436,688 bp (25.59%) number of C's = 33,276,187 bp (17.23%) number of T's = 64,407,936 bp (33.34%) number of G's = 46,036,769 bp (23.83%) number of N's = 20,516 bp (0.01%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,234,811 number of insertions = 12,737 mapped reads with insertion percentage = 0.4% number of deletions = 52,323 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.0624X std coverageData = 0.5887X There is a 2.84% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 15690072 0.06294897857044858 0.7184876758511791 chr2 243199373 18795117 0.07728275269854416 0.842076427772287 chr3 198022430 14581672 0.07363646633363706 0.5149726788697716 chr4 191154276 11159546 0.05837978743410375 0.49709744090888514 chr5 180915260 13592780 0.07513340776228605 0.5227993676009913 chr6 171115067 11793399 0.06892086831839303 0.5401162629293135 chr7 159138663 10640312 0.06686189138085193 0.6250337564204281 chr8 146364022 9764368 0.0667128975179433 0.8101100580185855 chr9 141213431 7983830 0.056537327529418924 0.5195955524350081 chr10 135534747 6979688 0.051497406786762956 0.5064976281964501 chr11 135006516 9399032 0.06961909897741528 0.5880872693407149 chr12 133851895 8062343 0.06023331234869704 0.47016948068579967 chr13 115169878 6210461 0.05392435164340453 0.4469318979858807 chr14 107349540 6336149 0.05902353191266586 0.4710585608511522 chr15 102531392 5858218 0.057135847721642166 0.48144997461618444 chr16 90354753 5203694 0.05759181257459693 0.4627120223887883 chr17 81195210 5060285 0.06232245719913773 0.4938066560860112 chr18 78077248 5441497 0.06969376021040086 0.8356897364444922 chr19 59128983 3375576 0.05708834870371439 0.5797223817420174 chr20 63025520 3518117 0.055820515245253034 0.4628148456495672 chr21 48129895 2737529 0.056877934182071245 0.4818428464665546 chr22 51304566 2087250 0.04068351343231322 0.38565556556685987 chrMT 16571 394163 23.786313439140667 16.682837565685265 chrX 155270560 7060438 0.04547183960694159 0.42628772206336196 chrY 59373566 1545253 0.0260259422518095 0.32381954932846724