BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163095.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 = 86,425,608 number of mapped reads = 84,997,510 (98.35%) number of supplementary alignments = 401,340 (0.46%) number of secondary alignments = 0 number of mapped bases = 7,649,490,217 bp number of sequenced bases = 7,648,641,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,105,839 duplication rate = 51.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6635 >>>>>>> ACTG content number of A's = 1,846,269,776 bp (24.14%) number of C's = 1,982,069,000 bp (25.91%) number of T's = 1,796,487,273 bp (23.49%) number of G's = 2,023,526,297 bp (26.46%) number of N's = 289,556 bp (0%) GC percentage = 52.37% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 28,605,576 number of insertions = 478,977 mapped reads with insertion percentage = 0.56% number of deletions = 384,444 mapped reads with deletion percentage = 0.45% homopolymer indels = 44.83% >>>>>>> Coverage mean coverageData = 2.471X std coverageData = 38.5218X There is a 7.67% of reference with a coverageData >= 1X There is a 5.58% of reference with a coverageData >= 2X There is a 3.95% of reference with a coverageData >= 3X There is a 3.55% of reference with a coverageData >= 4X There is a 3.16% of reference with a coverageData >= 5X There is a 2.96% of reference with a coverageData >= 6X There is a 2.78% of reference with a coverageData >= 7X There is a 2.64% of reference with a coverageData >= 8X There is a 2.52% of reference with a coverageData >= 9X There is a 2.42% of reference with a coverageData >= 10X There is a 2.33% of reference with a coverageData >= 11X There is a 2.25% of reference with a coverageData >= 12X There is a 2.18% of reference with a coverageData >= 13X There is a 2.11% of reference with a coverageData >= 14X There is a 2.05% of reference with a coverageData >= 15X There is a 1.99% of reference with a coverageData >= 16X There is a 1.94% of reference with a coverageData >= 17X There is a 1.89% of reference with a coverageData >= 18X There is a 1.84% of reference with a coverageData >= 19X There is a 1.79% of reference with a coverageData >= 20X There is a 1.75% of reference with a coverageData >= 21X There is a 1.71% of reference with a coverageData >= 22X There is a 1.67% of reference with a coverageData >= 23X There is a 1.64% of reference with a coverageData >= 24X There is a 1.6% of reference with a coverageData >= 25X There is a 1.57% of reference with a coverageData >= 26X There is a 1.54% of reference with a coverageData >= 27X There is a 1.51% of reference with a coverageData >= 28X There is a 1.48% of reference with a coverageData >= 29X There is a 1.45% of reference with a coverageData >= 30X There is a 1.42% of reference with a coverageData >= 31X There is a 1.4% of reference with a coverageData >= 32X There is a 1.37% of reference with a coverageData >= 33X There is a 1.35% of reference with a coverageData >= 34X There is a 1.32% of reference with a coverageData >= 35X There is a 1.3% of reference with a coverageData >= 36X There is a 1.28% of reference with a coverageData >= 37X There is a 1.26% of reference with a coverageData >= 38X There is a 1.24% of reference with a coverageData >= 39X There is a 1.22% of reference with a coverageData >= 40X There is a 1.2% of reference with a coverageData >= 41X There is a 1.18% of reference with a coverageData >= 42X There is a 1.16% of reference with a coverageData >= 43X There is a 1.14% of reference with a coverageData >= 44X There is a 1.12% of reference with a coverageData >= 45X There is a 1.11% of reference with a coverageData >= 46X There is a 1.09% of reference with a coverageData >= 47X There is a 1.08% of reference with a coverageData >= 48X There is a 1.06% of reference with a coverageData >= 49X There is a 1.04% of reference with a coverageData >= 50X There is a 1.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1156183104 4.638636804038294 50.96291503595734 chr2 243199373 317968593 1.3074400195924847 18.414573126188362 chr3 198022430 294698556 1.488207957048098 19.129448299734367 chr4 191154276 149404096 0.7815890867123475 13.84921912036842 chr5 180915260 417479287 2.3075957605787374 38.730598380559755 chr6 171115067 401760392 2.347896062244478 29.587624826088614 chr7 159138663 505190042 3.1745273742811326 43.505909853382214 chr8 146364022 483355917 3.302423029889135 89.0049042548511 chr9 141213431 337366461 2.389053637539619 28.229976583503344 chr10 135534747 177595783 1.3103339691924167 24.909006908909195 chr11 135006516 412707084 3.0569419627123775 32.22397184400206 chr12 133851895 200384822 1.4970637658884096 18.566508649267146 chr13 115169878 100160943 0.8696800303982262 13.827681594502787 chr14 107349540 215258268 2.0052090395543383 24.31945538310668 chr15 102531392 329870634 3.217264757314521 32.52463007046236 chr16 90354753 347119091 3.841735818811878 37.855046374251174 chr17 81195210 210760413 2.5957247108542485 27.534353935360738 chr18 78077248 123623609 1.5833499792410717 21.049979389417445 chr19 59128983 666794296 11.276945115054659 105.38103028773693 chr20 63025520 191255069 3.0345655061632177 33.1335259133927 chr21 48129895 99488900 2.0670915654397333 40.89975847632525 chr22 51304566 91516492 1.7837884448725285 21.89069934245146 chrMT 16571 3647 0.22008327801581076 0.6702536943497379 chrX 155270560 412232365 2.6549293375382943 38.3119633312199 chrY 59373566 7312353 0.12315839341703007 7.344777365197292