BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094140.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 = 2,434 number of mapped reads = 2,175 (89.36%) number of supplementary alignments = 166 (6.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,107 number of mapped paired reads (second in pair) = 1,068 number of mapped paired reads (both in pair) = 2,098 number of mapped paired reads (singletons) = 77 number of mapped bases = 276,721 bp number of sequenced bases = 271,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 996 duplication rate = 28.48% >>>>>>> Insert size mean insert size = 769,828.883 std insert size = 7,015,153.3964 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 21.9342 >>>>>>> ACTG content number of A's = 81,058 bp (29.9%) number of C's = 61,395 bp (22.65%) number of T's = 65,738 bp (24.25%) number of G's = 62,893 bp (23.2%) number of N's = 0 bp (0%) GC percentage = 45.85% >>>>>>> Mismatches and indels general error rate = 0.0376 number of mismatches = 9,742 number of insertions = 138 mapped reads with insertion percentage = 6.11% number of deletions = 756 mapped reads with deletion percentage = 33.33% homopolymer indels = 28.97% >>>>>>> Coverage mean coverageData = 0.0001X std coverageData = 0.0328X There is a 0% 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 3874 1.554258915968759E-5 0.009993755484983602 chr2 243199373 14903 6.12789408795063E-5 0.022395446161642008 chr3 198022430 4802 2.424977816906903E-5 0.008529881313472511 chr4 191154276 4761 2.4906583831794587E-5 0.007519316995514546 chr5 180915260 3725 2.0589750140480134E-5 0.012999202301737478 chr6 171115067 5259 3.073370505707718E-5 0.014210327182830424 chr7 159138663 7460 4.68773575155649E-5 0.017409180104030073 chr8 146364022 5304 3.6238413836427645E-5 0.0103588871005584 chr9 141213431 3953 2.799308799458318E-5 0.010306036765909063 chr10 135534747 5233 3.86100252210601E-5 0.011946331367527157 chr11 135006516 8215 6.0848914877560426E-5 0.02197226787746815 chr12 133851895 17604 1.315184966189683E-4 0.09467387821836337 chr13 115169878 5506 4.780763942460719E-5 0.01390617330983147 chr14 107349540 2268 2.1127244699884134E-5 0.01065966073573214 chr15 102531392 7231 7.052474231501705E-5 0.020838500668434342 chr16 90354753 1572 1.7398088620750256E-5 0.00551782298491149 chr17 81195210 5078 6.254063509411454E-5 0.018027499392792384 chr18 78077248 304 3.8935798556834384E-6 0.0024298958959457703 chr19 59128983 1283 2.1698326859435413E-5 0.009468420936446635 chr20 63025520 3367 5.3422803968931953E-5 0.02100852429872918 chr21 48129895 2156 4.479544366344452E-5 0.014529769403761978 chr22 51304566 471 9.180469434241E-6 0.003995423276148738 chrMT 16571 6693 0.40389837668215556 2.4269314932776673 chrX 155270560 153277 9.871607341404578E-4 0.0972789298618833 chrY 59373566 2422 4.079256415220201E-5 0.011789812196267943