{"text_format":"3","workbook":"xls","n_sheets":2,"sheets":["false negatives","false positives"],"read":"whole","date_system":"1900","formulas":"cached_only"}

{"sheet":"false negatives","index":0,"n_rows":20,"n_cols":7,"rows_kept":20,"merged":[[1,0,1,9],[2,1,2,2],[2,3,2,4],[2,5,2,6]],"flags":["formulas_cached_only"]}
["Table S4. Univariate error analysis."]
["For each in silico tumour, Pearson correlation between the number of teams with a false negative and the feature value (rows) at given breakpoints. P-values measuring the significance of the correlations are also shown. For the categorical features, trinucleotide and genomic location, the P-value measures the significance of the feature in a fitted binomial model predicting the false negative rate at a breakpoint. Abbreviations: SNP, single-nucleotide polymorphism; INDEL, short insertion or deletion.\n"]
["Feature","IS1",null,"IS2",null,"IS3"]
[null,"Correlation","P","Correlation","P","Correlation","P"]
["Reference allele count",{"v":0.11058927004671901,"d":"0.111"},{"v":3.98953052460627e-06,"d":"3.99E-06"},{"v":-0.0565874868167294,"d":"-0.057"},{"v":1.36397550637723e-08,"d":"1.36E-08"},{"v":-0.0309246132711639,"d":"-0.031"},{"v":0.0036970571230361,"d":"3.70E-03"}]
["Alternate allele count",{"v":0.005724363457806731,"d":"0.006"},{"v":0.81188598100753,"d":"8.12E-01"},{"v":-0.09602882551074139,"d":"-0.096"},{"v":4.921077362100541e-22,"d":"4.92E-22"},{"v":-0.0166755566653003,"d":"-0.017"},{"v":0.11756388173177201,"d":"1.18E-01"}]
["Base quality",{"v":0.106440674977439,"d":"0.106"},{"v":9.08372978303262e-06,"d":"9.08E-06"},{"v":-0.0346288994800563,"d":"-0.035"},{"v":0.0005149881430869701,"d":"5.15E-04"},{"v":-0.0113660154363949,"d":"-0.011"},{"v":0.28610033764235704,"d":"2.86E-01"}]
["Tumour coverage",{"v":0.106762863524562,"d":"0.107"},{"v":8.53048190485595e-06,"d":"8.53E-06"},{"v":-0.0660037447807036,"d":"-0.066"},{"v":3.48253741869119e-11,"d":"3.48E-11"},{"v":-0.0725295403833615,"d":"-0.073"},{"v":9.301888951495091e-12,"d":"9.30E-12"}]
["Normal coverage",{"v":0.0695795073462742,"d":"0.070"},{"v":0.00377597393502471,"d":"3.78E-03"},{"v":0.0181256024063806,"d":"0.018"},{"v":0.0691603442772917,"d":"6.92E-02"},{"v":-0.0240692927541032,"d":"-0.024"},{"v":0.0238477175233422,"d":"2.38E-02"}]
["Mapping quality",{"v":-0.0331786705254306,"d":"-0.033"},{"v":0.167651049439899,"d":"1.68E-01"},{"v":-0.0321841618931169,"d":"-0.032"},{"v":0.0012486437705154301,"d":"1.25E-03"},{"v":0.0384267454249994,"d":"0.038"},{"v":0.000308292240752239,"d":"3.08E-04"}]
["Read position",{"v":-0.00781127150883265,"d":"-0.008"},{"v":0.746503028720718,"d":"7.47E-01"},{"v":0.0146623141505446,"d":"0.015"},{"v":0.14281359003121402,"d":"1.43E-01"},{"v":0.0159232673985349,"d":"0.016"},{"v":0.135209071803851,"d":"1.35E-01"}]
["Trinucleotide","NA",{"v":0.8105449250558381,"d":"8.11E-01"},"NA",{"v":0.42448949573759504,"d":"4.24E-01"},"NA",{"v":0.00036662907429922404,"d":"3.67E-04"}]
["Homopolymer rate",{"v":-0.0415864954925245,"d":"-0.042"},{"v":0.0836809305140018,"d":"8.37E-02"},{"v":-0.0156805136334724,"d":"-0.016"},{"v":0.11590868244525301,"d":"1.16E-01"},{"v":-0.0412975756770404,"d":"-0.041"},{"v":0.00010530969091371001,"d":"1.05E-04"}]
["GC content",{"v":-0.0115295471497149,"d":"-0.012"},{"v":0.631682863871869,"d":"6.32E-01"},{"v":-0.146564308914777,"d":"-0.147"},{"v":2.15639450183119e-49,"d":"2.16E-49"},{"v":-0.00108034043109487,"d":"-0.001"},{"v":0.9192286588988631,"d":"9.19E-01"}]
["Genomic location","NA",{"v":0.441486663126859,"d":"4.41E-01"},"NA",{"v":0.00911587864872621,"d":"9.12E-03"},"NA",{"v":0.6603659717665781,"d":"6.60E-01"}]
["Bridging reads count",{"v":0.101829555285915,"d":"0.102"},{"v":2.1895930672810603e-05,"d":"2.19E-05"},{"v":-0.0670454074456332,"d":"-0.067"},{"v":1.70416779264878e-11,"d":"1.70E-11"},{"v":0.0311724498890327,"d":"0.031"},{"v":0.0034258989878290804,"d":"3.43E-03"}]
["Distance to germline INDEL",{"v":0.0780140922295811,"d":"0.078"},{"v":0.0011605363591833402,"d":"1.16E-03"},{"v":0.10222683630906301,"d":"0.102"},{"v":0,"d":"0.00E+00"},{"v":0.0942836713250908,"d":"0.094"},{"v":0,"d":"0.00E+00"}]
["Distance to germline SNP",{"v":0.00422785285314841,"d":"0.004"},{"v":0.8604709020652771,"d":"8.60E-01"},{"v":-0.0230413883886843,"d":"-0.023"},{"v":0.0208676190109376,"d":"2.09E-02"},{"v":-0.0142770447622788,"d":"-0.014"},{"v":0.180189239557788,"d":"1.80E-01"}]
["Nucleotide complexity",{"v":0.057072669488181,"d":"0.057"},{"v":0.017561062106934002,"d":"1.76E-02"},{"v":0.10922362486917701,"d":"0.109"},{"v":0,"d":"0.00E+00"},{"v":0.0249764618804813,"d":"0.025"},{"v":0.019039179783706398,"d":"1.90E-02"}]
["Strand bias",{"v":-0.0287304956567264,"d":"-0.029"},{"v":0.23436832833312402,"d":"2.34E-01"},{"v":-0.0847792105439197,"d":"-0.085"},{"v":2.1039606099150602e-17,"d":"2.10E-17"},{"v":0.0924664682119278,"d":"0.092"},{"v":0,"d":"0.00E+00"}]

{"sheet":"false positives","index":1,"n_rows":20,"n_cols":7,"rows_kept":20,"merged":[[1,0,1,9],[2,1,2,2],[2,3,2,4],[2,5,2,6]],"flags":["formulas_cached_only"]}
["Table S4. Univariate error analysis."]
["For each in silico tumour, Pearson correlation between the number of teams with a false positive and the feature value (rows) at given breakpoints. P-values measuring the significance of the correlations are also shown. For the categorical features, trinucleotide and genomic location, the P-value measures the significance of the feature in a fitted binomial model predicting the false positive rate at a breakpoint. Abbreviations: SNP, single-nucleotide polymorphism; INDEL, short insertion or deletion."]
["Feature","IS1",null,"IS2",null,"IS3"]
[null,"Correlation","P","Correlation","P","Correlation","P"]
["Reference allele count",{"v":-0.136432801648756,"d":"-0.136"},{"v":1.20588572183322e-08,"d":"1.21E-08"},{"v":0.17585616766064802,"d":"0.176"},{"v":0,"d":"0.00E+00"},{"v":0.11134010185961601,"d":"0.111"},{"v":0,"d":"0.00E+00"}]
["Alternate allele count",{"v":-0.0310724104897675,"d":"-0.031"},{"v":0.19630356607350902,"d":"1.96E-01"},{"v":0.42008519285879903,"d":"0.420"},{"v":0,"d":"0.00E+00"},{"v":0.0197482621630682,"d":"0.020"},{"v":0.0638076886608958,"d":"6.38E-02"}]
["Base quality",{"v":-0.12250777236294201,"d":"-0.123"},{"v":3.17826400149661e-07,"d":"3.18E-07"},{"v":0.0770844337439378,"d":"0.077"},{"v":9.992007221626412e-15,"d":"9.99E-15"},{"v":0.0832357001255021,"d":"0.083"},{"v":5.107025913275721e-15,"d":"5.11E-15"}]
["Tumour coverage",{"v":-0.11342185254692601,"d":"-0.113"},{"v":2.2362225272378e-06,"d":"2.24E-06"},{"v":0.24884687300558703,"d":"0.249"},{"v":0,"d":"0.00E+00"},{"v":0.25138537665576705,"d":"0.251"},{"v":0,"d":"0.00E+00"}]
["Normal coverage",{"v":-0.035601192154303296,"d":"-0.036"},{"v":0.13871393388164902,"d":"1.39E-01"},{"v":0.18011884627365,"d":"0.180"},{"v":0,"d":"0.00E+00"},{"v":0.120292269471807,"d":"0.120"},{"v":0,"d":"0.00E+00"}]
["Mapping quality",{"v":-0.047953403893547006,"d":"-0.048"},{"v":0.0460623411893882,"d":"4.61E-02"},{"v":-0.34821426219308405,"d":"-0.348"},{"v":1.6517824406491202e-284,"d":"1.65E-284"},{"v":-0.29820691011079703,"d":"-0.298"},{"v":1.8414239929752298e-180,"d":"1.84E-180"}]
["Read position",{"v":-0.0121313297779736,"d":"-0.012"},{"v":0.6156382721750241,"d":"6.16E-01"},{"v":-0.18519310003418402,"d":"-0.185"},{"v":8.77706019166009e-78,"d":"8.78E-78"},{"v":-0.0287792360306481,"d":"-0.029"},{"v":0.00692628943142387,"d":"6.93E-03"}]
["Trinucleotide","NA",{"v":0.9981283768490611,"d":"9.98E-01"},"NA",{"v":0.0320660445135017,"d":"3.21E-02"},"NA",{"v":0.36889454784031805,"d":"3.69E-01"}]
["Homopolymer rate",{"v":0.0752317142550967,"d":"0.075"},{"v":0.00173492418626209,"d":"1.73E-03"},{"v":0.0062665731203289604,"d":"0.006"},{"v":0.5298237725375771,"d":"5.30E-01"},{"v":0.0580539488187461,"d":"0.058"},{"v":4.930717611983941e-08,"d":"4.93E-08"}]
["GC content",{"v":0.050169697086641596,"d":"0.050"},{"v":0.0368762723462528,"d":"3.69E-02"},{"v":0.51810183191447,"d":"0.518"},{"v":0,"d":"0.00E+00"},{"v":0.0770391445131566,"d":"0.077"},{"v":4.42312853010662e-13,"d":"4.42E-13"}]
["Genomic location","NA",{"v":0.5967555691201221,"d":"5.97E-01"},"NA",{"v":0.0038713409165423204,"d":"3.87E-03"},"NA",{"v":0.42768621773056403,"d":"4.28E-01"}]
["Bridging reads count",{"v":-0.10862360208965201,"d":"-0.109"},{"v":5.91347810559854e-06,"d":"5.91E-06"},{"v":0.21472820360028302,"d":"0.215"},{"v":0,"d":"0.00E+00"},{"v":0.24276524285556303,"d":"0.243"},{"v":0,"d":"0.00E+00"}]
["Distance to germline INDEL",{"v":-0.143922928868315,"d":"-0.144"},{"v":1.7992060460520301e-09,"d":"1.80E-09"},{"v":-0.151963442407707,"d":"-0.152"},{"v":5.2456277941790605e-53,"d":"5.25E-53"},{"v":-0.0171140888798074,"d":"-0.017"},{"v":0.108159924105324,"d":"1.08E-01"}]
["Distance to germline SNP",{"v":0.040637770646968004,"d":"0.041"},{"v":0.0909852978915076,"d":"9.10E-02"},{"v":0.0736059747565335,"d":"0.074"},{"v":1.4743761767022102e-13,"d":"1.47E-13"},{"v":0.0872422392520181,"d":"0.087"},{"v":2.2204460492503099e-16,"d":"2.22E-16"}]
["Nucleotide complexity",{"v":-0.0537440693937477,"d":"-0.054"},{"v":0.0253492590214204,"d":"2.53E-02"},{"v":-0.311878472756143,"d":"-0.312"},{"v":3.5997031063513e-225,"d":"3.60E-225"},{"v":-0.0258315275656511,"d":"-0.026"},{"v":0.0153057750414982,"d":"1.53E-02"}]
["Strand bias",{"v":0.0765584114450111,"d":"0.077"},{"v":0.00150963279923699,"d":"1.51E-03"},{"v":0.045416929665648496,"d":"0.045"},{"v":5.59358043084046e-06,"d":"5.59E-06"},{"v":0.0267209444963612,"d":"0.027"},{"v":0.0121752727036686,"d":"1.22E-02"}]