BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472796.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 108,394,740 number of mapped reads = 107,962,899 (99.6%) number of supplementary alignments = 74,147 (0.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 54,112,053 number of mapped paired reads (second in pair) = 53,850,846 number of mapped paired reads (both in pair) = 107,665,106 number of mapped paired reads (singletons) = 297,793 number of mapped bases = 10,687,241,930 bp number of sequenced bases = 10,686,042,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,049,156 duplication rate = 48.2% >>>>>>> Insert size mean insert size = 12,648.5814 std insert size = 1,128,480.0153 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 53.5276 >>>>>>> ACTG content number of A's = 2,880,636,352 bp (26.96%) number of C's = 2,459,965,719 bp (23.02%) number of T's = 2,926,505,132 bp (27.39%) number of G's = 2,417,784,866 bp (22.63%) number of N's = 1,150,444 bp (0.01%) GC percentage = 45.65% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 41,925,193 number of insertions = 420,373 mapped reads with insertion percentage = 0.38% number of deletions = 491,875 mapped reads with deletion percentage = 0.45% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 3.4523X std coverageData = 25.2876X There is a 15.35% of reference with a coverageData >= 1X There is a 8.73% of reference with a coverageData >= 2X There is a 5.72% of reference with a coverageData >= 3X There is a 4.96% of reference with a coverageData >= 4X There is a 4.43% of reference with a coverageData >= 5X There is a 4.21% of reference with a coverageData >= 6X There is a 4.02% of reference with a coverageData >= 7X There is a 3.88% of reference with a coverageData >= 8X There is a 3.77% of reference with a coverageData >= 9X There is a 3.67% of reference with a coverageData >= 10X There is a 3.58% of reference with a coverageData >= 11X There is a 3.49% of reference with a coverageData >= 12X There is a 3.42% of reference with a coverageData >= 13X There is a 3.34% of reference with a coverageData >= 14X There is a 3.28% of reference with a coverageData >= 15X There is a 3.21% of reference with a coverageData >= 16X There is a 3.15% of reference with a coverageData >= 17X There is a 3.1% of reference with a coverageData >= 18X There is a 3.04% of reference with a coverageData >= 19X There is a 2.99% of reference with a coverageData >= 20X There is a 2.94% of reference with a coverageData >= 21X There is a 2.89% of reference with a coverageData >= 22X There is a 2.85% of reference with a coverageData >= 23X There is a 2.8% of reference with a coverageData >= 24X There is a 2.76% of reference with a coverageData >= 25X There is a 2.72% of reference with a coverageData >= 26X There is a 2.67% of reference with a coverageData >= 27X There is a 2.63% of reference with a coverageData >= 28X There is a 2.6% of reference with a coverageData >= 29X There is a 2.56% of reference with a coverageData >= 30X There is a 2.52% of reference with a coverageData >= 31X There is a 2.49% of reference with a coverageData >= 32X There is a 2.45% of reference with a coverageData >= 33X There is a 2.42% of reference with a coverageData >= 34X There is a 2.39% of reference with a coverageData >= 35X There is a 2.35% of reference with a coverageData >= 36X There is a 2.32% of reference with a coverageData >= 37X There is a 2.29% of reference with a coverageData >= 38X There is a 2.26% of reference with a coverageData >= 39X There is a 2.23% of reference with a coverageData >= 40X There is a 2.2% of reference with a coverageData >= 41X There is a 2.18% of reference with a coverageData >= 42X There is a 2.15% of reference with a coverageData >= 43X There is a 2.12% of reference with a coverageData >= 44X There is a 2.09% of reference with a coverageData >= 45X There is a 2.07% of reference with a coverageData >= 46X There is a 2.04% of reference with a coverageData >= 47X There is a 2.02% of reference with a coverageData >= 48X There is a 1.99% of reference with a coverageData >= 49X There is a 1.97% of reference with a coverageData >= 50X There is a 1.95% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1203465659 4.828335649362334 33.582204042650304 chr2 243199373 878977071 3.6142242480205735 26.783706965395695 chr3 198022430 708982744 3.5803153410449515 26.743041220870307 chr4 191154276 304303421 1.591925785641332 13.144379812128712 chr5 180915260 477496831 2.6393397162848506 19.79534881043889 chr6 171115067 658774211 3.8498901502344034 27.642585874463748 chr7 159138663 599264205 3.7656732418318732 29.747501659976365 chr8 146364022 385020731 2.630569492002618 20.755666502599833 chr9 141213431 485601008 3.438773525727875 25.435063484827854 chr10 135534747 458985061 3.3864752114083334 24.38092118210251 chr11 135006516 426458624 3.158800305608953 19.48104893831293 chr12 133851895 527760251 3.942867233967812 23.791263768577892 chr13 115169878 393627504 3.4177990880566878 31.761305552420612 chr14 107349540 229491946 2.13780092583536 15.52741210282603 chr15 102531392 275838577 2.6902841326878697 18.116384133239283 chr16 90354753 416411789 4.608631811543993 29.646802540880373 chr17 81195210 481663815 5.932170321377333 28.52161092278948 chr18 78077248 139686896 1.789085803843906 15.274162301452453 chr19 59128983 483760291 8.18144108786718 35.603040186584614 chr20 63025520 412958462 6.552242044175121 39.82766603276176 chr21 48129895 119697364 2.486964993378855 22.381685027117573 chr22 51304566 196931278 3.838474688588146 23.90193315928451 chrMT 16571 458241 27.65318930662 80.52584695017842 chrX 155270560 380684221 2.4517475882098965 20.395232449386132 chrY 59373566 40941729 0.6895615634742235 11.131704582602614