BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618648.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 66,294,719 number of mapped reads = 64,674,658 (97.56%) number of supplementary alignments = 91,602 (0.14%) number of secondary alignments = 0 number of mapped bases = 6,330,369,033 bp number of sequenced bases = 6,326,535,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,750,482 duplication rate = 50.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.1326 >>>>>>> ACTG content number of A's = 1,718,240,046 bp (27.16%) number of C's = 1,452,270,795 bp (22.96%) number of T's = 1,876,300,390 bp (29.66%) number of G's = 1,278,186,990 bp (20.2%) number of N's = 1,536,804 bp (0.02%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 48,932,960 number of insertions = 1,011,028 mapped reads with insertion percentage = 1.54% number of deletions = 2,610,799 mapped reads with deletion percentage = 3.95% homopolymer indels = 52.25% >>>>>>> Coverage mean coverageData = 2.0449X std coverageData = 49.3723X There is a 12.3% of reference with a coverageData >= 1X There is a 8.77% of reference with a coverageData >= 2X There is a 7.09% of reference with a coverageData >= 3X There is a 6.03% of reference with a coverageData >= 4X There is a 5.28% of reference with a coverageData >= 5X There is a 4.73% of reference with a coverageData >= 6X There is a 4.29% of reference with a coverageData >= 7X There is a 3.93% of reference with a coverageData >= 8X There is a 3.62% of reference with a coverageData >= 9X There is a 3.36% of reference with a coverageData >= 10X There is a 3.12% of reference with a coverageData >= 11X There is a 2.9% of reference with a coverageData >= 12X There is a 2.7% of reference with a coverageData >= 13X There is a 2.52% of reference with a coverageData >= 14X There is a 2.35% of reference with a coverageData >= 15X There is a 2.2% of reference with a coverageData >= 16X There is a 2.05% of reference with a coverageData >= 17X There is a 1.93% of reference with a coverageData >= 18X There is a 1.81% of reference with a coverageData >= 19X There is a 1.71% of reference with a coverageData >= 20X There is a 1.62% of reference with a coverageData >= 21X There is a 1.54% of reference with a coverageData >= 22X There is a 1.47% of reference with a coverageData >= 23X There is a 1.4% of reference with a coverageData >= 24X There is a 1.34% of reference with a coverageData >= 25X There is a 1.29% of reference with a coverageData >= 26X There is a 1.23% of reference with a coverageData >= 27X There is a 1.18% of reference with a coverageData >= 28X There is a 1.14% of reference with a coverageData >= 29X There is a 1.09% of reference with a coverageData >= 30X There is a 1.05% of reference with a coverageData >= 31X There is a 1.02% of reference with a coverageData >= 32X There is a 0.98% of reference with a coverageData >= 33X There is a 0.95% of reference with a coverageData >= 34X There is a 0.91% of reference with a coverageData >= 35X There is a 0.88% of reference with a coverageData >= 36X There is a 0.86% of reference with a coverageData >= 37X There is a 0.83% of reference with a coverageData >= 38X There is a 0.81% of reference with a coverageData >= 39X There is a 0.78% of reference with a coverageData >= 40X There is a 0.76% of reference with a coverageData >= 41X There is a 0.74% of reference with a coverageData >= 42X There is a 0.72% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.66% of reference with a coverageData >= 46X There is a 0.65% of reference with a coverageData >= 47X There is a 0.63% of reference with a coverageData >= 48X There is a 0.62% of reference with a coverageData >= 49X There is a 0.6% of reference with a coverageData >= 50X There is a 0.59% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 655457306 2.629711827277654 76.95139979539528 chr2 243199373 560258971 2.303702366041873 56.01940834968534 chr3 198022430 438238719 2.213076160109741 53.93427708938072 chr4 191154276 310128865 1.6224008768707847 37.50152131293668 chr5 180915260 388817345 2.1491683178080168 63.727300380409616 chr6 171115067 350918818 2.050776849475213 41.11198664560802 chr7 159138663 313575573 1.9704549924489436 38.98166703876865 chr8 146364022 328617736 2.2452084297054915 53.09162311491204 chr9 141213431 278825240 1.9744951880674864 46.122749396684085 chr10 135534747 314682105 2.3217817715777342 49.71297692438931 chr11 135006516 341966280 2.5329612979569074 58.295352435227706 chr12 133851895 312640345 2.335718481983389 55.11613441708725 chr13 115169878 171653647 1.4904387325998556 34.15301143983301 chr14 107349540 196924792 1.8344260441171896 42.93825155477311 chr15 102531392 192355209 1.8760616163291726 31.968173299329493 chr16 90354753 226599097 2.5078824242926103 43.01484656298019 chr17 81195210 204615831 2.5200480545588833 42.47300511700998 chr18 78077248 168863584 2.162775819147724 44.85665300303558 chr19 59128983 134154033 2.268837145397884 34.921135423312485 chr20 63025520 182396038 2.894002905489713 46.78896582589427 chr21 48129895 78813949 1.6375258869773142 29.90787171042468 chr22 51304566 111700154 2.177197132902362 40.887710276878266 chrMT 16571 43107 2.601351759097218 13.759856098420396 chrX 155270560 10558861 0.0680029813765082 4.71923945016641 chrY 59373566 57563428 0.9695127289474241 23.164780688615487