BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506317.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 = 4,066,642 number of mapped reads = 3,425,489 (84.23%) number of supplementary alignments = 58,555 (1.44%) number of secondary alignments = 0 number of mapped bases = 270,924,868 bp number of sequenced bases = 270,811,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 506,965 duplication rate = 10.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9957 >>>>>>> ACTG content number of A's = 71,837,050 bp (26.53%) number of C's = 50,726,446 bp (18.73%) number of T's = 82,150,100 bp (30.33%) number of G's = 66,046,387 bp (24.39%) number of N's = 51,378 bp (0.02%) GC percentage = 43.12% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,864,340 number of insertions = 21,743 mapped reads with insertion percentage = 0.62% number of deletions = 58,128 mapped reads with deletion percentage = 1.67% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.0875X std coverageData = 0.688X There is a 5.64% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 19521555 0.0783209884159125 1.2934643756078594 chr2 243199373 21246349 0.08736185763110499 0.7016917344711256 chr3 198022430 17589370 0.08882513965715905 0.4288015187414272 chr4 191154276 18351295 0.09600253462287184 0.5595896461582054 chr5 180915260 22158163 0.12247813147437094 0.5145451277591178 chr6 171115067 8695989 0.050819540046698516 0.3630884535504332 chr7 159138663 13276967 0.08343017812082536 0.6354948867378789 chr8 146364022 17119786 0.1169671738045023 0.8821017130589542 chr9 141213431 5913786 0.04187835362487581 0.6008764188112237 chr10 135534747 15482521 0.11423285425102096 0.7541764550809064 chr11 135006516 10945331 0.0810726128211471 0.6455601957617425 chr12 133851895 11389860 0.08509300522043413 0.43421601590856834 chr13 115169878 5857683 0.050861241686823704 0.3202646635140911 chr14 107349540 8046743 0.07495833703619037 0.4440966229704579 chr15 102531392 10124669 0.09874701593829917 0.46939974584337146 chr16 90354753 10429583 0.11542926800984117 0.5818500493367142 chr17 81195210 6595377 0.08122864636965653 0.48153673536086555 chr18 78077248 4989675 0.06390690153423441 1.1413679671551153 chr19 59128983 7654964 0.1294621285808349 0.9798725168476352 chr20 63025520 6673290 0.10588234734120401 0.5044638601236593 chr21 48129895 4599276 0.09555965164686106 0.5511255667977856 chr22 51304566 3643868 0.0710242437291059 0.4071413073270194 chrMT 16571 13772 0.8310904592360148 1.306711168770786 chrX 155270560 19658831 0.12661016357511687 0.5776124796853126 chrY 59373566 946165 0.015935795400936505 0.5468441052821166