BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708615.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,806,086 number of mapped reads = 2,789,306 (73.29%) number of supplementary alignments = 848 (0.02%) number of secondary alignments = 0 number of mapped bases = 135,841,046 bp number of sequenced bases = 135,815,126 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,003 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3143 >>>>>>> ACTG content number of A's = 39,974,623 bp (29.43%) number of C's = 25,594,541 bp (18.85%) number of T's = 42,907,388 bp (31.59%) number of G's = 27,326,623 bp (20.12%) number of N's = 11,951 bp (0.01%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 843,429 number of insertions = 6,432 mapped reads with insertion percentage = 0.23% number of deletions = 17,141 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.53% >>>>>>> Coverage mean coverageData = 0.0439X std coverageData = 0.4624X There is a 3.64% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 10807015 0.043358026377795865 0.8785306596833977 chr2 243199373 11515057 0.04734821828673053 0.4622780803288016 chr3 198022430 9415183 0.047546043142688434 0.25772368344294017 chr4 191154276 9222536 0.04824655871156133 0.26481851155774894 chr5 180915260 8616369 0.0476265462625983 0.26197788542999256 chr6 171115067 8068291 0.04715125991798256 0.34576030406748426 chr7 159138663 7788141 0.04893933914726932 0.6774888441186468 chr8 146364022 7122827 0.048665149417662215 0.8072202867562359 chr9 141213431 5677401 0.040204398121309014 0.36358949892376513 chr10 135534747 6328017 0.04668925969220277 0.3600170680750727 chr11 135006516 6094179 0.04513988791474331 0.3961876779506756 chr12 133851895 6067728 0.04533165555855597 0.2643128260574364 chr13 115169878 4672885 0.04057384692202244 0.2402467592045187 chr14 107349540 4065326 0.03786998994127036 0.25203684242587254 chr15 102531392 3778061 0.03684784656000769 0.2240947548964097 chr16 90354753 3518497 0.03894091769582946 0.25463771724248474 chr17 81195210 3265663 0.040219897208222014 0.2844180131828787 chr18 78077248 3851122 0.049324510003221425 0.744774983633392 chr19 59128983 2303754 0.03896150217905828 0.6456196904550608 chr20 63025520 2628952 0.041712499952400235 0.2538607941293728 chr21 48129895 1781487 0.03701414682080648 0.24869573668611364 chr22 51304566 1332022 0.025963030269079753 0.1847021890798875 chrMT 16571 20722 1.2504978577032164 1.491121601257945 chrX 155270560 7595212 0.0489159825275313 0.30380615867565675 chrY 59373566 304599 0.005130212323780586 0.09570557557424612