BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819022.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,274,104 number of mapped reads = 1,255,276 (98.52%) number of supplementary alignments = 20,404 (1.6%) number of secondary alignments = 0 number of mapped bases = 116,058,072 bp number of sequenced bases = 115,985,184 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 415,956 duplication rate = 28.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2166 >>>>>>> ACTG content number of A's = 33,277,974 bp (28.69%) number of C's = 24,515,213 bp (21.14%) number of T's = 33,265,629 bp (28.68%) number of G's = 24,920,423 bp (21.49%) number of N's = 5,945 bp (0.01%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 748,813 number of insertions = 18,905 mapped reads with insertion percentage = 1.46% number of deletions = 38,715 mapped reads with deletion percentage = 3.01% homopolymer indels = 40.16% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.4805X There is a 2.22% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 11754363 0.04715881129138691 0.8464163986896096 chr2 243199373 9415353 0.03871454471225137 0.7020251535471111 chr3 198022430 6209744 0.03135879102180495 0.27082040401699414 chr4 191154276 6433870 0.033657996748134474 0.32594800245819466 chr5 180915260 6226955 0.03441918056000362 0.29271994712535127 chr6 171115067 4813518 0.028130299011015786 0.3065027475299221 chr7 159138663 5702632 0.03583435912113953 0.5339080348390381 chr8 146364022 10629880 0.07262631796221068 0.4498395043451512 chr9 141213431 4956256 0.035097624672825914 0.41024677038961627 chr10 135534747 6188175 0.04565747999662404 0.6316314754605447 chr11 135006516 3935913 0.02915350396865289 0.3034277256469427 chr12 133851895 5348703 0.03995986011255201 0.310069891796358 chr13 115169878 2479591 0.021529856964856733 0.22182207856256184 chr14 107349540 2729727 0.025428399600035546 0.2641765274382191 chr15 102531392 2986956 0.02913211204623068 0.2625776427850136 chr16 90354753 3705763 0.04101348160400593 0.5799180038871337 chr17 81195210 4069633 0.050121589684908756 0.38395389069196156 chr18 78077248 2715836 0.03478396164782857 0.4992104842464149 chr19 59128983 2457392 0.04155985568025075 0.7587008648322113 chr20 63025520 3376825 0.05357869320237263 0.3829180345286854 chr21 48129895 1555024 0.032308900736226415 0.3019283486331952 chr22 51304566 918383 0.017900609470120066 0.23162061807203804 chrMT 16571 14161 0.8545652042725242 1.4806508108355578 chrX 155270560 6978849 0.044946376183611365 0.3752686455779705 chrY 59373566 454570 0.007656100696394082 0.5350732673083337