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["Additional file 2.  Empirical estimation of error rates for the E. coli amplicon library.  Statistics are for raw reads, filtered and trimmed as listed. All quality values are listed as Phred quality scores. Variant bases were identified using VarScan. N50, the sequence read length at which > 50% of all bases reside in sequence reads longer than the listed value.  N95,  the sequence read length at which > 95% of all bases reside in sequence reads longer than the listed value."]
[]
[null,null,"Length Stats1"]
["Filtering Criteria","Reads surviving filter","N50","N95","Avg. length","Total base pairs "]
["minimum 50bp reads2",{"v":2676,"d":"2,676"},374,184,274.46,{"v":733911,"d":"733,911"}]
["minimum 300bp reads",{"v":1831,"d":"1,831"},375,371,373.41,{"v":683708,"d":"683,708"}]
["minimum 300bp/Q20 reads3",215,375,369,372.1,{"v":80001,"d":"80,001"}]
["minimum 300bp/Q163",724,374,371,371.72,{"v":269122,"d":"269,122"}]
["minimum 400bp reads",{"v":1765,"d":"1,765"},375,372,374.88,{"v":661657,"d":"661,657"}]
["minimum 360bp/ maximum expected error 1.5",894,360,360,360,{"v":321840,"d":"321,840"}]
[]
[null,null,"Quality Stats"]
[null,"% bases > Q20","% bases > Q30","Min Q","Max Q","Avg. Q"]
["minimum 50bp reads",87.04,57.28,5,45,28.19]
["minimum 300bp reads",89.41,60.31,5,45,28.71]
["minimum 300bp/Q20 reads",95.93,69.82,7,45,30.17]
["minimum 300bp/Q16",92.31,65.37,7,45,29.53]
["minimum 400bp reads",89.75,60.87,6,45,28.79]
["minimum 360bp/ maximum expected error 1.5",94.71,69.95,7,45,30.08]
[]
[null,null,"Error Stats"]
["Filtering Criteria","Total Substitutions","Total Indels","Total errors","Max indel freq./site","Max subs. freq./site"]
["minimum 50bp reads",445,{"v":4568,"d":"4,568"},5013,0.6239,0.0219]
["minimum 300bp reads",405,{"v":3505,"d":"3,505"},3910,0.572,0.0231]
["minimum 300bp/Q20 reads",42,154,196,0.2698,0.0093]
["minimum 300bp/Q16",158,872,1030,0.5104,0.0042]
["minimum 400bp reads",340,{"v":3219,"d":"3,219"},3559,0.5655,0.0054]
["minimum 360bp/ maximum expected error 1.5",118,58,176,0.4518,0.0054]
[]
[null,null,"Error Stats cont."]
[null,"Per-base indel error rate","Per-base substitution error rate","Per-base combined error rate"]
["minimum 50bp reads",{"v":0.006224187946494875,"d":"0.006"},{"v":0.0006063405508297328,"d":"0.001"},{"v":0.0068305284973246075,"d":"0.007"}]
["minimum 300bp reads",{"v":0.005126457493549878,"d":"0.005"},{"v":0.000592358141194779,"d":"0.001"},{"v":0.005718815634744657,"d":"0.006"}]
["minimum 300bp/Q20 reads",{"v":0.0019249759378007776,"d":"0.002"},{"v":0.0005249934375820303,"d":"0.001"},{"v":0.002449969375382808,"d":"0.002"}]
["minimum 300bp/Q16",{"v":0.0032401661699898187,"d":"0.003"},{"v":0.0005870943289660452,"d":"0.001"},{"v":0.003827260498955864,"d":"0.004"}]
["minimum 400bp reads",{"v":0.004865058481962709,"d":"0.005"},{"v":0.0005138614115772976,"d":"0.001"},{"v":0.005378919893540006,"d":"0.005"}]
["minimum 360bp/ maximum expected error 1.5",{"v":0.00018021377081779767,"d":"0.000"},{"v":0.0003666418095948297,"d":"0.000"},{"v":0.0005468555804126274,"d":"0.001"}]
[]
[]
[]
["1All values are given for reads after barcode and primer removal"]
["2Retained only those reads 50bp or longer, etc."]
["3Quality filtering based on maintaining the average listed Q score for 10bp sliding window along read"]