BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 367,378 number of mapped reads = 341,336 (92.91%) number of supplementary alignments = 11,647 (3.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 171,566 number of mapped paired reads (second in pair) = 169,770 number of mapped paired reads (both in pair) = 338,396 number of mapped paired reads (singletons) = 2,940 number of mapped bases = 45,011,683 bp number of sequenced bases = 43,890,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 325,776 duplication rate = 48.49% >>>>>>> Insert size mean insert size = 276,817.1701 std insert size = 4,672,389.729 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 36.2335 >>>>>>> ACTG content number of A's = 11,572,918 bp (26.37%) number of C's = 10,346,973 bp (23.57%) number of T's = 11,002,984 bp (25.07%) number of G's = 10,967,165 bp (24.99%) number of N's = 375 bp (0%) GC percentage = 48.56% >>>>>>> Mismatches and indels general error rate = 0.0439 number of mismatches = 1,875,991 number of insertions = 26,479 mapped reads with insertion percentage = 7.66% number of deletions = 146,739 mapped reads with deletion percentage = 40.97% homopolymer indels = 28.41% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 4.2098X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% 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% 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 588225 0.0023599740600044484 1.173166474675683 chr2 243199373 1760117 0.0072373418495614295 2.9084364882943845 chr3 198022430 727151 0.0036720638162050633 1.3793066119328663 chr4 191154276 415972 0.002176106173005515 1.1219113284654474 chr5 180915260 477192 0.002637654778264697 1.3962429960340834 chr6 171115067 946565 0.005531745489133344 3.8718563939430837 chr7 159138663 2059857 0.012943787268088335 5.009611811529964 chr8 146364022 1035497 0.0070748055830277745 2.2584561071152125 chr9 141213431 505202 0.0035775775464304102 1.806165195966061 chr10 135534747 838803 0.006188841006210755 2.877216917415089 chr11 135006516 1274018 0.00943671489159827 2.8427091101554267 chr12 133851895 1040919 0.007776647465469204 2.695218369522763 chr13 115169878 1038516 0.00901725362598717 2.783128919843554 chr14 107349540 317171 0.0029545631960789026 1.3205631687181771 chr15 102531392 777155 0.0075796786217434756 2.689925749925397 chr16 90354753 299194 0.003311325525952132 1.2942081980608244 chr17 81195210 991490 0.012211188320099178 3.321486330306009 chr18 78077248 141753 0.0018155481094825473 0.5275184629449647 chr19 59128983 209686 0.003546247362312996 0.8219101462860408 chr20 63025520 326564 0.005181456654383811 1.7122842070795792 chr21 48129895 593476 0.012330714621338775 4.943794307848125 chr22 51304566 68320 0.0013316553540283335 0.3488470616839608 chrMT 16571 905294 54.631223221290206 258.52601760628573 chrX 155270560 27438290 0.17671276512430947 15.017938001490831 chrY 59373566 235256 0.0039623020116393215 1.0442343397794203