BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085138.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,545,873 number of mapped reads = 2,315,092 (90.94%) number of supplementary alignments = 23,350 (0.92%) number of secondary alignments = 0 number of mapped bases = 156,942,572 bp number of sequenced bases = 156,884,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,891 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.775 >>>>>>> ACTG content number of A's = 44,539,042 bp (28.39%) number of C's = 29,039,747 bp (18.51%) number of T's = 49,325,786 bp (31.44%) number of G's = 33,944,602 bp (21.64%) number of N's = 34,946 bp (0.02%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,379,078 number of insertions = 12,487 mapped reads with insertion percentage = 0.53% number of deletions = 35,915 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.3967X There is a 4.43% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 12612566 0.05060194413718231 0.630617147134222 chr2 243199373 13094585 0.053843004767944035 0.4671369994761016 chr3 198022430 10862331 0.054854043554560965 0.25914371679172643 chr4 191154276 10215594 0.05344161906166305 0.2678765178373252 chr5 180915260 9762002 0.05395897504721271 0.2589090777625664 chr6 171115067 9448697 0.05521838120777523 0.3053854574453384 chr7 159138663 8758127 0.05503456441631661 0.46544933832986896 chr8 146364022 8176789 0.05586611305338412 0.7481941903446758 chr9 141213431 6900515 0.04886585469338253 0.3569106953939979 chr10 135534747 7495497 0.055303139349203195 0.365482494301516 chr11 135006516 7014536 0.05195701813385067 0.33677201221350306 chr12 133851895 6935279 0.051813080419967156 0.2544789356226473 chr13 115169878 5119206 0.04444917446209329 0.23610803906846736 chr14 107349540 4867968 0.045346892031395754 0.24991295514232 chr15 102531392 4261747 0.04156528958467666 0.23088011175610162 chr16 90354753 4185273 0.046320452007654764 0.2652836743046277 chr17 81195210 3969215 0.048884841852124036 0.26563774486476194 chr18 78077248 4254385 0.05448943333658481 0.6448723269214542 chr19 59128983 2873749 0.04860136018236606 0.5309498973332326 chr20 63025520 3099689 0.04918149029155174 0.24985609824491076 chr21 48129895 2230054 0.04633407157858956 0.25242644999806746 chr22 51304566 1645305 0.03206936786094244 0.1961626940316416 chrMT 16571 14014 0.8456942851970309 0.9225588234449695 chrX 155270560 8767910 0.05646859262953647 0.29130524583711837 chrY 59373566 377539 0.006358705151716843 0.13839246434112293