BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231826.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 = 1,545,064 number of mapped reads = 946,172 (61.24%) number of supplementary alignments = 7,777 (0.5%) number of secondary alignments = 0 number of mapped bases = 59,698,392 bp number of sequenced bases = 59,656,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,196 duplication rate = 7.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9336 >>>>>>> ACTG content number of A's = 16,549,518 bp (27.74%) number of C's = 9,834,083 bp (16.48%) number of T's = 20,204,826 bp (33.87%) number of G's = 13,059,725 bp (21.89%) number of N's = 7,960 bp (0.01%) GC percentage = 38.38% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 609,939 number of insertions = 5,316 mapped reads with insertion percentage = 0.55% number of deletions = 24,338 mapped reads with deletion percentage = 2.53% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 0.3243X There is a 1.44% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 5590927 0.02243094511688298 0.31700157089741354 chr2 243199373 3646452 0.014993673523985607 0.22108675951944098 chr3 198022430 5019619 0.02534873953420327 0.2046434722786696 chr4 191154276 2734670 0.014306088554357005 0.16286165734277316 chr5 180915260 3326420 0.018386619238200248 0.1752015146384001 chr6 171115067 3840411 0.02244344152347496 0.2627849263548834 chr7 159138663 3866007 0.02429332336416575 0.261826506162843 chr8 146364022 3028239 0.020689777163953583 1.1318637873002135 chr9 141213431 2266496 0.016050144691973387 0.19117506612321336 chr10 135534747 3673935 0.027106960254258638 0.23662638050023918 chr11 135006516 2639599 0.019551641492622476 0.1998824109201885 chr12 133851895 2354241 0.017588402465277014 0.17098549548225356 chr13 115169878 2791096 0.024234600647922887 0.2071434626355921 chr14 107349540 2962398 0.027595814569862154 0.21840521740330804 chr15 102531392 1032830 0.01007330515906777 0.1276123842769104 chr16 90354753 1383223 0.01530880174062343 0.16598046939664357 chr17 81195210 1475561 0.01817300552581858 0.1796480228741297 chr18 78077248 1281084 0.016407904131047243 0.31153133986562315 chr19 59128983 1372931 0.023219256113368295 0.2315791354753544 chr20 63025520 1239317 0.019663733040203395 0.18352770432917878 chr21 48129895 1005615 0.020893770908912226 0.1889361636583941 chr22 51304566 434555 0.008470103811033115 0.11470885959404314 chrMT 16571 56037 3.381630559411019 3.3126773759959183 chrX 155270560 2470284 0.015909545247985196 0.1718528940160875 chrY 59373566 206445 0.0034770523973581104 0.08119114507353893