BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971302.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,368,745 number of mapped reads = 7,065,619 (84.43%) number of secondary alignments = 0 number of mapped bases = 278,804,569 bp number of sequenced bases = 278,776,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 370,914 duplication rate = 4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6301 >>>>>>> ACTG content number of A's = 81,507,678 bp (29.24%) number of C's = 56,419,348 bp (20.24%) number of T's = 83,216,727 bp (29.85%) number of G's = 57,616,726 bp (20.67%) number of N's = 15,608 bp (0.01%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 819,625 number of insertions = 9,528 mapped reads with insertion percentage = 0.13% number of deletions = 22,691 mapped reads with deletion percentage = 0.32% homopolymer indels = 40.98% >>>>>>> Coverage mean coverageData = 0.0901X std coverageData = 0.7582X There is a 7.37% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 20995020 0.08423256847171506 1.316574639228945 chr2 243199373 23088566 0.09493678258783998 0.6135761219287988 chr3 198022430 18699705 0.09443225699230133 0.37190927739223156 chr4 191154276 18308932 0.09578091781739688 0.41609125000346986 chr5 180915260 17403179 0.09619519657987945 0.37504258430730397 chr6 171115067 16331854 0.09544369345336493 0.3984956594151906 chr7 159138663 15772533 0.09911188584008651 1.0655687581264275 chr8 146364022 13784031 0.09417636118253159 1.7127099169187843 chr9 141213431 11167378 0.07908155705104283 0.6218398943716654 chr10 135534747 13051134 0.09629363900314065 0.7029506923602749 chr11 135006516 12310635 0.09118548766935071 0.6060849772750265 chr12 133851895 12362838 0.09236206928560854 0.37357167241697375 chr13 115169878 8836011 0.07672154519430853 0.31731305447979713 chr14 107349540 18736941 0.17454141862182176 0.5467377537289871 chr15 102531392 7646311 0.0745753164065109 0.316239523581867 chr16 90354753 7147006 0.07909939170549224 0.4259459935188508 chr17 81195210 6662757 0.08205849827840829 0.3823193324714727 chr18 78077248 8445683 0.10817085919831601 1.2526884006486754 chr19 59128983 4717353 0.07978072276331896 1.2037341304869047 chr20 63025520 5132577 0.08143648794964325 0.3597131217952937 chr21 48129895 3604675 0.0748947197994095 0.40846611366681806 chr22 51304566 2744647 0.05349712928085192 0.29516787720598664 chrMT 16571 17689 1.0674672620843642 1.3468655929272384 chrX 155270560 9544111 0.061467614981230184 0.3727411193198301 chrY 59373566 2293003 0.038619930627040326 0.3878588990741528