BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094084.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 = 395,466 number of mapped reads = 381,003 (96.34%) number of supplementary alignments = 11,049 (2.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 191,456 number of mapped paired reads (second in pair) = 189,547 number of mapped paired reads (both in pair) = 378,326 number of mapped paired reads (singletons) = 2,677 number of mapped bases = 51,161,372 bp number of sequenced bases = 50,069,008 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 363,400 duplication rate = 48.23% >>>>>>> Insert size mean insert size = 255,837.9652 std insert size = 4,586,258.7723 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 38.1177 >>>>>>> ACTG content number of A's = 13,251,617 bp (26.47%) number of C's = 11,928,610 bp (23.82%) number of T's = 12,655,758 bp (25.28%) number of G's = 12,232,324 bp (24.43%) number of N's = 699 bp (0%) GC percentage = 48.26% >>>>>>> Mismatches and indels general error rate = 0.0398 number of mismatches = 1,919,638 number of insertions = 27,848 mapped reads with insertion percentage = 7.2% number of deletions = 152,832 mapped reads with deletion percentage = 38.27% homopolymer indels = 30.03% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 4.8098X 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 430352 0.0017265834615513354 0.7894246753107681 chr2 243199373 2950869 0.012133538683095206 5.308606034040252 chr3 198022430 924407 0.004668193396071344 1.9369730916794614 chr4 191154276 594248 0.0031087350617257444 1.4175094161734314 chr5 180915260 458103 0.0025321412909005024 1.2427896301674666 chr6 171115067 949883 0.0055511359499394635 3.62764146877971 chr7 159138663 1938218 0.012179428703633133 4.49925197569636 chr8 146364022 647945 0.00442694175211993 1.3953373185113225 chr9 141213431 792168 0.005609721358586635 2.072615652264143 chr10 135534747 887114 0.006545288345873402 1.9698960953056057 chr11 135006516 1700999 0.012599384462302545 4.180372386912888 chr12 133851895 1457173 0.010886457752428533 4.348690486476091 chr13 115169878 1457788 0.012657719408194563 3.888141810655856 chr14 107349540 248858 0.002318202760812948 1.073334327479801 chr15 102531392 928695 0.009057664992980882 2.718306086982437 chr16 90354753 205062 0.0022695208961503108 0.7994605917953259 chr17 81195210 1177873 0.014506680874401335 4.64811542080771 chr18 78077248 106042 0.001358167746895997 0.47769327458354044 chr19 59128983 210406 0.0035584241318677846 0.913402107712864 chr20 63025520 256195 0.004064940677998373 1.2826989371606594 chr21 48129895 957939 0.019903201534098507 8.713053359601146 chr22 51304566 55414 0.0010800987966646087 0.3641105214962282 chrMT 16571 2583789 155.92233419829824 729.4920127388941 chrX 155270560 28664453 0.18460970965777415 14.6799379081884 chrY 59373566 577379 0.00972451275707442 2.8077901847788205