BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094134.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 = 538,374 number of mapped reads = 521,592 (96.88%) number of supplementary alignments = 9,502 (1.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 261,744 number of mapped paired reads (second in pair) = 259,848 number of mapped paired reads (both in pair) = 519,076 number of mapped paired reads (singletons) = 2,516 number of mapped bases = 75,405,668 bp number of sequenced bases = 75,220,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 520,945 duplication rate = 40.54% >>>>>>> Insert size mean insert size = 138,286.8533 std insert size = 3,331,410.7906 median insert size = 229 >>>>>>> Mapping quality mean mapping quality = 23.5538 >>>>>>> ACTG content number of A's = 21,148,639 bp (28.12%) number of C's = 16,076,939 bp (21.37%) number of T's = 21,359,254 bp (28.4%) number of G's = 16,634,488 bp (22.11%) number of N's = 1,014 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0173 number of mismatches = 1,253,790 number of insertions = 28,852 mapped reads with insertion percentage = 5.46% number of deletions = 64,621 mapped reads with deletion percentage = 12.09% homopolymer indels = 54.51% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 34.9468X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 60894 2.443083180924151E-4 0.0652512939216151 chr2 243199373 255567 0.0010508538605483986 0.8040290413048459 chr3 198022430 61967 3.129291969601625E-4 0.11324527015724671 chr4 191154276 196414 0.0010275155968784084 0.6782664187148792 chr5 180915260 600501 0.003319239073586164 2.974613591734462 chr6 171115067 312447 0.0018259467472843873 1.373546331917221 chr7 159138663 254728 0.0016006669604859002 0.8362310931931055 chr8 146364022 104998 7.173757496224038E-4 0.47431422777929916 chr9 141213431 24064 1.704087198334555E-4 0.041585582462887245 chr10 135534747 46699 3.4455371064366245E-4 0.09084207105363884 chr11 135006516 1800604 0.013337163666974414 6.095011158817655 chr12 133851895 458608 0.0034262346453892193 2.3040547673980845 chr13 115169878 2426743 0.021070986981509176 16.74257573818039 chr14 107349540 105560 9.833297841797925E-4 0.323896924313812 chr15 102531392 1976401 0.019276057424442262 16.09170975329792 chr16 90354753 236305 0.002615302373744522 2.2706863503065073 chr17 81195210 745826 0.009185591120461417 4.931095003135523 chr18 78077248 13737 1.7594113972869534E-4 0.060893787416877725 chr19 59128983 12300 2.080198132276349E-4 0.036001241136415695 chr20 63025520 9489 1.5055805965583465E-4 0.026653997837287658 chr21 48129895 4736 9.840038088593379E-5 0.016870563607047917 chr22 51304566 56055 0.0010925928113298922 0.5384811743763509 chrMT 16571 58282498 3517.1382535755233 14508.606409405907 chrX 155270560 7293525 0.04697300634453821 10.911576633938155 chrY 59373566 65002 0.0010947969673911788 0.43339346065333073