BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961006.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 388,865,150 number of mapped reads = 381,088,636 (98%) number of supplementary alignments = 814,622 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 190,789,602 number of mapped paired reads (second in pair) = 190,299,034 number of mapped paired reads (both in pair) = 380,022,508 number of mapped paired reads (singletons) = 1,066,128 number of mapped bases = 37,199,476,376 bp number of sequenced bases = 37,188,000,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,720,252 duplication rate = 12.05% >>>>>>> Insert size mean insert size = 15,704.0973 std insert size = 1,198,544.4414 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 53.5888 >>>>>>> ACTG content number of A's = 11,021,678,386 bp (29.64%) number of C's = 7,553,274,482 bp (20.31%) number of T's = 10,966,867,722 bp (29.49%) number of G's = 7,627,577,188 bp (20.51%) number of N's = 18,602,267 bp (0.05%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 199,675,044 number of insertions = 3,824,873 mapped reads with insertion percentage = 0.97% number of deletions = 4,498,641 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 12.0165X std coverageData = 142.0789X There is a 91.22% of reference with a coverageData >= 1X There is a 90.53% of reference with a coverageData >= 2X There is a 88.97% of reference with a coverageData >= 3X There is a 86.84% of reference with a coverageData >= 4X There is a 83.6% of reference with a coverageData >= 5X There is a 79.68% of reference with a coverageData >= 6X There is a 74.82% of reference with a coverageData >= 7X There is a 69.51% of reference with a coverageData >= 8X There is a 63.69% of reference with a coverageData >= 9X There is a 57.76% of reference with a coverageData >= 10X There is a 51.75% of reference with a coverageData >= 11X There is a 45.94% of reference with a coverageData >= 12X There is a 40.35% of reference with a coverageData >= 13X There is a 35.13% of reference with a coverageData >= 14X There is a 30.29% of reference with a coverageData >= 15X There is a 25.91% of reference with a coverageData >= 16X There is a 21.97% of reference with a coverageData >= 17X There is a 18.49% of reference with a coverageData >= 18X There is a 15.45% of reference with a coverageData >= 19X There is a 12.82% of reference with a coverageData >= 20X There is a 10.58% of reference with a coverageData >= 21X There is a 8.68% of reference with a coverageData >= 22X There is a 7.09% of reference with a coverageData >= 23X There is a 5.77% of reference with a coverageData >= 24X There is a 4.68% of reference with a coverageData >= 25X There is a 3.79% of reference with a coverageData >= 26X There is a 3.07% of reference with a coverageData >= 27X There is a 2.48% of reference with a coverageData >= 28X There is a 2.01% of reference with a coverageData >= 29X There is a 1.63% of reference with a coverageData >= 30X There is a 1.33% of reference with a coverageData >= 31X There is a 1.09% of reference with a coverageData >= 32X There is a 0.9% of reference with a coverageData >= 33X There is a 0.75% of reference with a coverageData >= 34X There is a 0.63% of reference with a coverageData >= 35X There is a 0.53% of reference with a coverageData >= 36X There is a 0.46% of reference with a coverageData >= 37X There is a 0.4% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.31% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3212051466 12.886834356171976 341.5524108925507 chr2 243199373 3842209536 15.798599678133217 82.97918771402657 chr3 198022430 2378736507 12.012459936987947 41.73959593632208 chr4 191154276 1982051281 10.368856624478545 116.86508138189396 chr5 180915260 1954108192 10.801234743824264 13.17529580343443 chr6 171115067 2209175469 12.910467253009346 41.4447688001432 chr7 159138663 1914654431 12.03135928696347 87.9435846294636 chr8 146364022 2084322030 14.240672000664206 133.1652484301432 chr9 141213431 1879575374 13.310174256724915 95.22785458404445 chr10 135534747 1641735427 12.113022404505614 350.35763829291045 chr11 135006516 1659514728 12.292108389790608 54.494069738048545 chr12 133851895 1871127050 13.979085241938487 12.831025222500037 chr13 115169878 1009388712 8.764346455242404 7.683306739060187 chr14 107349540 741619904 6.908459076769216 12.385041263404094 chr15 102531392 940919596 9.176892829076191 7.341582773283433 chr16 90354753 1074406602 11.890980455671214 133.89160119539082 chr17 81195210 902915923 11.120310212880785 36.946474660923286 chr18 78077248 1137650565 14.570833298325269 126.12709533652094 chr19 59128983 775560344 13.116416089889453 172.12301118585088 chr20 63025520 786957266 12.486327221100279 37.75493781698885 chr21 48129895 458038089 9.516706591610058 64.37251538518305 chr22 51304566 516156463 10.060634037913896 11.29841159291559 chrMT 16571 17564423 1059.9494900730192 183.19216027945123 chrX 155270560 2088120532 13.448270760406867 42.6420024666233 chrY 59373566 120916466 2.0365370340060087 124.68986337394443