BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083631.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,720,751 number of mapped reads = 1,527,601 (88.78%) number of supplementary alignments = 16,573 (0.96%) number of secondary alignments = 0 number of mapped bases = 100,766,522 bp number of sequenced bases = 100,729,969 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,324 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1704 >>>>>>> ACTG content number of A's = 26,994,364 bp (26.8%) number of C's = 18,817,619 bp (18.68%) number of T's = 31,690,814 bp (31.46%) number of G's = 23,222,213 bp (23.05%) number of N's = 4,959 bp (0%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 679,668 number of insertions = 7,379 mapped reads with insertion percentage = 0.48% number of deletions = 22,418 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.56% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.2508X There is a 2.7% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 10806282 0.04335508556265543 0.33738166002147724 chr2 243199373 9669134 0.03975805480386662 0.3969414412088955 chr3 198022430 6122704 0.030919244855241904 0.2085316612349984 chr4 191154276 4051276 0.02119375032970751 0.1731181687378763 chr5 180915260 5400445 0.02985068810668597 0.20290570145599607 chr6 171115067 7365388 0.043043480209723435 0.27349517789881483 chr7 159138663 5932965 0.03728173209548707 0.2870982724805016 chr8 146364022 7861258 0.053710316870084374 0.2967003000457696 chr9 141213431 3721505 0.026353760925191316 0.2062595802022066 chr10 135534747 4335266 0.03198638058475145 0.2224747369747186 chr11 135006516 3775335 0.0279640947108064 0.20888726824924558 chr12 133851895 3629883 0.02711865229849753 0.1932948653139189 chr13 115169878 2749514 0.023873551381204033 0.18238952073557815 chr14 107349540 2808953 0.02616641859853335 0.18972031173953763 chr15 102531392 2749473 0.02681591409585076 0.19765139908856666 chr16 90354753 3883761 0.0429834720482275 0.2488329031128151 chr17 81195210 1955263 0.024081014138641922 0.1838189980224083 chr18 78077248 1801317 0.02307095916085567 0.2400223234933459 chr19 59128983 2461886 0.04163585901688855 0.29506725974858683 chr20 63025520 2381521 0.03778661405728981 0.23024279581960083 chr21 48129895 1314400 0.027309430033038717 0.19573940965134476 chr22 51304566 474426 0.009247247116367771 0.11049405693877871 chrMT 16571 5615 0.3388449701285378 0.6970885033000629 chrX 155270560 5313293 0.03421957774867303 0.2223779051846429 chrY 59373566 195659 0.0032953890625333168 0.07430780585076126