BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818864.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,704,266 number of mapped reads = 1,610,705 (94.51%) number of supplementary alignments = 25,026 (1.47%) number of secondary alignments = 0 number of mapped bases = 149,238,358 bp number of sequenced bases = 149,144,242 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 372,515 duplication rate = 19.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3607 >>>>>>> ACTG content number of A's = 43,338,472 bp (29.06%) number of C's = 30,468,416 bp (20.43%) number of T's = 42,326,087 bp (28.38%) number of G's = 33,009,244 bp (22.13%) number of N's = 2,023 bp (0%) GC percentage = 42.56% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 904,858 number of insertions = 21,411 mapped reads with insertion percentage = 1.29% number of deletions = 48,847 mapped reads with deletion percentage = 2.96% homopolymer indels = 41.08% >>>>>>> Coverage mean coverageData = 0.0482X std coverageData = 0.5702X There is a 3.3% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 14226706 0.05707791596635581 0.8478854343005768 chr2 243199373 11883725 0.04886412680019533 0.8305735892178188 chr3 198022430 9303320 0.046981142489767445 0.2935320193125728 chr4 191154276 7650800 0.04002421583286999 0.34732994611175355 chr5 180915260 6614429 0.03656092360589151 0.27148100681002 chr6 171115067 7180470 0.04196281558303688 0.30576132784148974 chr7 159138663 13572740 0.08528876480506814 1.1921777454738443 chr8 146364022 12673880 0.08659149855830008 0.4994115617973599 chr9 141213431 5547834 0.039286872082302145 0.46693081377196477 chr10 135534747 6760353 0.04987911328745831 0.7471294723887751 chr11 135006516 6640633 0.04918749995740946 0.35317228093423675 chr12 133851895 5897189 0.04405756825482374 0.2892564903724626 chr13 115169878 4661427 0.04047435910282027 0.2688967177530386 chr14 107349540 4396667 0.04095655183990542 0.3086162238444269 chr15 102531392 4081238 0.03980476535420489 0.26747115728154536 chr16 90354753 3755426 0.04156312618108756 0.6294140518976238 chr17 81195210 4104047 0.05054543242144457 0.36762550183857995 chr18 78077248 2962214 0.03793952881126138 0.5459388317974793 chr19 59128983 2299827 0.038895088048444874 0.7306263366340507 chr20 63025520 5224102 0.08288867747540996 0.41657801983205517 chr21 48129895 1470638 0.030555603746902003 0.2807943398674264 chr22 51304566 1352406 0.02636034383372427 0.25377156834566444 chrMT 16571 199038 12.011224428217972 7.763029287329958 chrX 155270560 6224625 0.04008889386371763 0.33874486097417317 chrY 59373566 554624 0.00934126139568575 0.6563536274791747