BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818919.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 = 2,053,549 number of mapped reads = 1,994,412 (97.12%) number of supplementary alignments = 28,842 (1.4%) number of secondary alignments = 0 number of mapped bases = 184,808,629 bp number of sequenced bases = 184,691,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 498,626 duplication rate = 21.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3294 >>>>>>> ACTG content number of A's = 51,747,523 bp (28.02%) number of C's = 38,535,560 bp (20.86%) number of T's = 53,004,912 bp (28.7%) number of G's = 41,400,982 bp (22.42%) number of N's = 2,551 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,111,808 number of insertions = 25,298 mapped reads with insertion percentage = 1.23% number of deletions = 59,847 mapped reads with deletion percentage = 2.93% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0597X std coverageData = 0.745X There is a 3.95% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 17498909 0.07020607984764057 1.177768257027099 chr2 243199373 13812423 0.056794648890809436 1.0032663948322307 chr3 198022430 11452831 0.057836028979141405 0.3372369610993391 chr4 191154276 9299273 0.0486479988551237 0.41930682604960423 chr5 180915260 8191724 0.04527934238383208 0.3097149492360241 chr6 171115067 9111706 0.05324899881551635 0.35896551835645485 chr7 159138663 16448908 0.10336211006121121 1.6996084672166676 chr8 146364022 15967172 0.10909219206889519 0.6062578782925371 chr9 141213431 6791632 0.04809480197390006 0.5637854874955089 chr10 135534747 8509856 0.06278726443485375 0.9702040568355617 chr11 135006516 8090043 0.05992335214398096 0.43264417606903477 chr12 133851895 7173161 0.05359028349953506 0.328557895283898 chr13 115169878 5634776 0.04892577901315481 0.30485204042231734 chr14 107349540 5394916 0.050255604262486826 0.3393999844921237 chr15 102531392 5100093 0.04974177079347562 0.3099481662266053 chr16 90354753 5076328 0.056182191101778564 0.6771682398793811 chr17 81195210 4727930 0.05822917386382768 0.45002225393221257 chr18 78077248 3522018 0.04510940242156076 0.6973280160879468 chr19 59128983 3230774 0.05463943122444707 1.0629285455291808 chr20 63025520 7541754 0.11966190838250917 0.5229144938555536 chr21 48129895 1803208 0.03746544637174047 0.33051648282925417 chr22 51304566 1699744 0.03313046250113489 0.2781018809264599 chrMT 16571 456333 27.53804839780339 18.216428027886355 chrX 155270560 7581475 0.04882751115214629 0.38669106933865754 chrY 59373566 691642 0.011648988709891537 0.8393482904878209