BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549111.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,807,440 number of mapped reads = 10,072,563 (85.31%) number of secondary alignments = 0 number of mapped bases = 395,651,303 bp number of sequenced bases = 395,603,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 905,991 duplication rate = 6.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5501 >>>>>>> ACTG content number of A's = 116,830,113 bp (29.53%) number of C's = 80,267,020 bp (20.29%) number of T's = 117,449,414 bp (29.69%) number of G's = 81,055,801 bp (20.49%) number of N's = 1,543 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,648,491 number of insertions = 16,854 mapped reads with insertion percentage = 0.17% number of deletions = 38,815 mapped reads with deletion percentage = 0.39% homopolymer indels = 41.41% >>>>>>> Coverage mean coverageData = 0.1278X std coverageData = 1.3056X There is a 8.17% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 31596480 0.1267659028219633 2.098084705947552 chr2 243199373 34122545 0.14030687899840927 0.925643432145445 chr3 198022430 27117491 0.13694151213072175 0.5747578842891837 chr4 191154276 26168990 0.13689984104776187 0.6072915273786724 chr5 180915260 24978543 0.1380676400652991 0.5985282049600028 chr6 171115067 23263617 0.13595306017090827 0.6446041521373689 chr7 159138663 22439438 0.1410055707204226 1.3538997326846172 chr8 146364022 20875984 0.14263057078330357 3.627166915648269 chr9 141213431 16955050 0.12006683698521567 0.98474037341119 chr10 135534747 18628935 0.13744766867790736 0.9387503351719726 chr11 135006516 19697454 0.14590002455881462 0.8188201103416282 chr12 133851895 18284768 0.136604476163748 0.6340976449716719 chr13 115169878 12708151 0.11034266268824215 0.511627591972178 chr14 107349540 12268839 0.1142886965328403 1.5370234251685375 chr15 102531392 11559831 0.11274430956716164 0.5028586571014233 chr16 90354753 11080801 0.12263661436825576 0.628298875122278 chr17 81195210 10228938 0.12597957441085503 0.5731620889417373 chr18 78077248 10693996 0.13696686645512915 1.9024646472989495 chr19 59128983 7976952 0.134907647574456 2.196448233425798 chr20 63025520 8139141 0.1291404021735957 0.6167978886868715 chr21 48129895 5219098 0.10843775994109274 0.5932553661118977 chr22 51304566 4375182 0.08527860853554438 0.5014035494485755 chrMT 16571 183334 11.063544746846901 13.555870206577175 chrX 155270560 13812107 0.08895509232400527 0.6579320671655414 chrY 59373566 3275638 0.05516997244194496 0.491478651021541