BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818775.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,457,445 number of mapped reads = 2,396,504 (97.52%) number of supplementary alignments = 20,601 (0.84%) number of secondary alignments = 0 number of mapped bases = 162,743,259 bp number of sequenced bases = 162,678,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,569,936 duplication rate = 50.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7606 >>>>>>> ACTG content number of A's = 46,332,955 bp (28.48%) number of C's = 37,065,691 bp (22.78%) number of T's = 47,226,818 bp (29.03%) number of G's = 32,042,976 bp (19.7%) number of N's = 10,286 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 832,258 number of insertions = 15,801 mapped reads with insertion percentage = 0.65% number of deletions = 41,003 mapped reads with deletion percentage = 1.7% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.0526X std coverageData = 0.7123X There is a 1.4% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 12987055 0.05210440378401304 0.8106366389356012 chr2 243199373 20126876 0.0827587495466117 1.0716237182772386 chr3 198022430 10761853 0.05434663638861517 0.6287596391702348 chr4 191154276 10288899 0.053825105120850134 0.6738266257944826 chr5 180915260 9989700 0.055217564289491115 0.6388872191547651 chr6 171115067 9333233 0.05454360719737205 0.6535397832466215 chr7 159138663 8671238 0.054488568877821976 0.6951387347948146 chr8 146364022 7952729 0.05433527236631964 0.6697037989204857 chr9 141213431 6635507 0.04698920600548258 0.6489065383562734 chr10 135534747 7594788 0.056035726395682134 0.734706313985746 chr11 135006516 7490245 0.05548061843177999 0.6815299899353353 chr12 133851895 7144460 0.0533758599383296 0.6584193688587937 chr13 115169878 5140148 0.044631010202164145 0.5712137132066254 chr14 107349540 4922438 0.0458542998880107 0.6065250787881146 chr15 102531392 4423141 0.043139383107175605 0.5597639011739302 chr16 90354753 4445201 0.04919720161262574 0.7103089937186247 chr17 81195210 3936131 0.04847737939220799 0.62263632823963 chr18 78077248 4392140 0.05625377574783374 0.8116953759085417 chr19 59128983 2938040 0.049688661142708986 0.7615609146346433 chr20 63025520 3262227 0.0517604138767915 0.63739645230871 chr21 48129895 2091394 0.043453117859492525 0.583317150936789 chr22 51304566 1868717 0.036423990020693284 0.5738463081979867 chrMT 16571 126201 7.615774545893428 9.542620781477424 chrX 155270560 4884617 0.03145874530239345 0.48676617336422723 chrY 59373566 1336281 0.022506328826535364 0.9106942182756499