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{"sheet":"TableS5_Legend","index":0,"n_rows":40,"n_cols":2,"rows_kept":40,"cut":false,"hidden":false,"merged":[[0,0,6,1],[22,1,27,1],[28,1,33,1],[34,1,39,1]]}
["Additional file 6: Table S5. Prioritization of 37 non-coding pathogenic variants and their associated 37 internal control negative common variants spiked in within 100 individual genomes."]
{"$rows_empty":16}
["Column Name","Description"]
["Associated_gene","Name of the closest protein coding gene"]
["Associated_disease","Disease name(s) reported by HGMD/ClinVar"]
["Non_coding_region","Non-coding region associated with the variant position by ANNOVAR"]
["variant_id","Chomosome name:position of the variant (GRCh37 1-based ):Reference allele : Alternative allele"]
["NCBoost","Median rank percentile of each pathogenic or common variant against all scored variants of each of the 100 sampled individuals. "]
["Eigen"]
["FunSeq2"]
["CADD"]
["ReMM"]
["DeepSEA"]
["NCBoost_abs_rank","Median rank of each pathogenic or common variant against all scored variants of each of the 100 sampled individuals. "]
["Eigen_abs_rank"]
["FunSeq2_abs_rank"]
["CADD_abs_rank"]
["ReMM_abs_rank"]
["DeepSEA_abs_rank"]
["NCBoost_var_count","Median of the total number of background variants per individual for which the considered method could provide a score."]
["Eigen_var_count"]
["FunSeq2_var_count"]
["CADD_var_count"]
["ReMM_var_count"]
["DeepSEA_var_count"]

{"sheet":"TableS5","index":1,"n_rows":39,"n_cols":35,"rows_kept":39,"cut":false,"hidden":false,"merged":[[0,0,0,2],[0,3,0,15],[0,16,0,28],[0,29,0,34]]}
[null,null,null,"Pathogenic Variants",{"$nulls":12},"Common Variants",{"$nulls":12},"Shared between pathogenic and common variants"]
["Associated_gene","Associated_disease","Non_coding_region","variant_id","NCBoost","Eigen","FunSeq2","CADD","ReMM","DeepSEA","NCBoost_abs_rank","Eigen_abs_rank","FunSeq2_abs_rank","CADD_abs_rank","ReMM_abs_rank","DeepSEA_abs_rank","variant_id","NCBoost","Eigen","FunSeq2","CADD","ReMM","DeepSEA","NCBoost_abs_rank","Eigen_abs_rank","FunSeq2_abs_rank","CADD_abs_rank","ReMM_abs_rank","DeepSEA_abs_rank","NCBoost_var_count","Eigen_var_count","FunSeq2_var_count","CADD_var_count","ReMM_var_count","DeepSEA_var_count"]
["DHDDS","Congenital_disorder_of_glycosylation_type_1bb","intronic","1:26774026:A:G",97.21,96.765,96.83,98.96,97.91,99.15,1003170.5,997774.5,998336,1021237.5,1010288.5,1023205.5,"1:26785926:G:A",78.46,75.48,81.09,77.14,34.13,79.45,809891.5,778381.5,836041.5,796235,352214.5,820092.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["AGL","Glycogen_storage_disease_type_III|Glycogen_storage_disease_IIIa|Glycogen_storage_disease_IIIb","intronic","1:100381954:A:G",96.54,94.265,47.89,96.04,89,95.3,996300,971963,493557,990987.5,918501.5,983545.5,"1:100334848:C:T",28.02,61.97,47.48,57.49,81.95,27.645,289246.5,639138.5,489262,593463.5,845767,285197.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["USH2A","Usher_syndrome|Usher_syndrome,_type_2A|Retinitis_pigmentosa_39","intronic","1:216064540:T:C",99.92,99.76,87.43,98.29,99.88,99.95,1031164,1028707.5,901560,1014304,1030713,1031422,"1:216415521:A:G",51.955,5.64,23.275,9.55,7.8,17.39,536152.5,58126.5,239854.5,98547.5,80400,179438.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["CDH23","Usher_syndrome,_type_1D","intronic","10:73494416:G:T",99.91,100,83.16,100,99.9,99.4,1031013.5,1031184,857404,1031928,1030870.5,1025792,"10:73411591:G:T",59.36,52.43,35.11,55.58,59.04,70.08,612507,540491.5,361840,573637,609045,723355.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["HBB","Beta_thalassemia_intermedia|not_specified","intronic","11:5247102:A:C",75.625,84.41,50.68,19.33,53.04,58.86,780603,870477,522341,199474,547368,607447.5,"11:5247141:G:A",3.36,16.44,52.01,42.77,43.52,12.79,34649,169449.5,536021.5,441437.5,449345,131980.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["MYBPC3","Hypertrophic_cardiomyopathy|Primary_familial_hypertrophic_cardiomyopathy","intronic","11:47364815:T:C",100,100,94.14,100,99.88,96.99,1031928,1031184,970704.5,1031928,1030713,1000939.5,"11:47363285:G:A",82.33,78.28,64.96,46.51,7.8,33.73,849755.5,807289.5,669837.5,479918,80400,347989.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["MYBPC3","Familial_hypertrophic_cardiomyopathy_4","intronic","11:47368581:C:G",100,100,94.14,100,99.34,95.52,1031928,1031184,970704.5,1031925,1025100,985866,"11:47357170:G:A",56.39,43.695,64.96,21.99,32.59,55.38,581927,450515,669837.5,226954,336323.5,571534,1031931,1031184,1031013.5,1031931,1031931,1031931]
["MYBPC3","not_provided","intronic","11:47368581:C:T",100,100,94.14,100,99.34,93.62,1031928,1031184,970704.5,1031927.5,1025100,966042,"11:47362431:A:G",86.23,67.42,75.46,81.75,50.94,63.27,890042.5,695346.5,777706,843636,525836.5,652957.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["IGHMBP2","IGHMBP2-related_condition","intronic","11:68697719:C:A",80.69,15.28,41.8,14.26,7.8,49.54,832862,157500.5,430776.5,147192,80400,511179,"11:68680000:T:A",33.01,35.96,57.75,89.33,63.39,37.06,340665.5,370864,595136,921968.5,654081.5,382457.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["ATM","Ataxia-telangiectasia_syndrome|Hereditary_cancer-predisposing_syndrome|Ataxia-telangiectasia_variant","intronic","11:108179837:A:G",95.68,67.27,88.76,34.305,35.55,31.66,987456.5,693800.5,915215.5,353988.5,366838.5,326716.5,"11:108219339:C:A",63.755,15.59,88.78,93.13,30.98,17.63,657904,160696.5,915446,961104.5,319629,181969,1031931,1031184,1031013.5,1031931,1031931,1031931]
["NCAPD3","MICROCEPHALY_22,_PRIMARY,_AUTOSOMAL_RECESSIVE","intronic","11:134086816:T:C",99.26,83.42,35.11,80.76,90.695,75.21,1024346,860335.5,361840,833458,936040.5,776241.5,"11:134066752:T:C",0.42,7.65,39.105,15.95,50.57,51.635,4293.5,78860,402874.5,164636,522046.5,532856,1031931,1031184,1031013.5,1031931,1031931,1031931]
["CEP290","Leber_congenital_amaurosis","intronic","12:88508350:A:C",99.31,96.59,94.14,71.855,93.35,95.35,1024871,995946,970704.5,741769,963340,984129,"12:88517281:C:G",38.33,38.05,64.96,11.96,29.385,48.41,395418,392304.5,669837.5,123402.5,303177.5,499616,1031931,1031184,1031013.5,1031931,1031931,1031931]
["FBN1","Marfan_syndrome","intronic","15:48786466:G:T",32.69,60.99,59.63,32.79,58.31,43.43,337392.5,628951,614366.5,338305,601455,448226,"15:48750520:C:A",91.26,91.07,60.15,78.96,74.49,61.77,941909.5,939164,620075,814958,768706.5,637484,1031931,1031184,1031013.5,1031931,1031931,1031931]
["IFT140","Renal_dysplasia,_retinal_pigmentary_dystrophy,_cerebellar_ataxia_and_skeletal_dysplasia","intronic","16:1576595:C:T",99.03,91.1,89.835,86.58,87.615,91.71,1021980.5,939450.5,926273,893523.5,904222,946469,"16:1605606:C:T",96.14,85.46,32.62,77.9,80.47,91.6,992228.5,881356.5,336246,804025.5,830468,945289.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["CTNS","Nephropathic_cystinosis|Juvenile_nephropathic_cystinosis|Cystinosis,_ocular_nonnephropathic","intronic","17:3563518:G:A",99.97,99.14,95.95,91.98,98.89,95.68,1031580,1022289.5,989280.5,949135,1020441,987454.5,"17:3556594:C:T",59.21,47.55,64.96,58.765,76.92,57.905,610936.5,490226.5,669837.5,606585,793867.5,597543,1031931,1031184,1031013.5,1031931,1031931,1031931]
["CAMTA2","Dystonia with tremor","UTR5","17:4890930:C:T",97.04,100,99.07,99.63,99.92,100,1001402,1031168,1021414,1028120,1031146.5,1031902.5,"17:4890932:C:A",93.62,100,99.06,99.4,99.91,99.97,966132.5,1031166,1021350.5,1025735.5,1030964,1031643,1031931,1031184,1031013.5,1031931,1031931,1031931]
["TMEM107","Leukoencephalopathy,_brain_calcifications,_and_cysts","UTR3","17:8076849:T:C",99.97,99.92,99.97,93.5,99.94,99.55,1031625.5,1030378,1030738,964918.5,1031335,1027284,"17:8076655:C:T",68.51,90.67,99.81,70.45,93.48,63.34,707069,935083.5,1029010.5,727289,964677.5,653665.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["BRCA1","Breast-ovarian_cancer,_familial_1","intronic","17:41256988:T:C",98.73,98.78,98.21,98.95,98.85,94.66,1018826,1018633,1012519,1021111,1019979.5,976910,"17:41275151:G:C",26.535,49.63,91.64,16.4,83.3,93.28,273834,511664.5,945022.5,169200,859596.5,962614,1031931,1031184,1031013.5,1031931,1031931,1031931]
["DGKE","Hemolytic-uremic_syndrome","intronic","17:54925466:A:G",87,86.87,33.04,86.71,80.33,84.43,898032,895897,340923.5,894824.5,829027.5,871311.5,"17:54926338:C:T",93.18,74.89,82.92,73.75,39.91,77.66,961654,772311,854843.5,761367.5,411965.5,801618,1031931,1031184,1031013.5,1031931,1031931,1031931]
["LDLR","Familial_hypercholesterolemia","intronic","19:11231284:C:G",72.55,59.19,98.27,52.37,45.68,67.95,748745,610408,1013090.5,540450,471581.5,701280,"19:11232951:A:T",62.79,37.97,84.365,8.27,64.12,6.1,647931.5,391559,869908,85400.5,661507.5,62973.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["FKRP","Limb-girdle_muscular_dystrophy-dystroglycanopathy,_type_C5","UTR5","19:47249328:G:A",95.69,99.33,98.48,97.59,95.65,99.07,987554.5,1024233,1015265,1006988,987101,1022365.5,"19:47251930:C:G",37.245,81.1,87.1,66.12,95.04,99.59,384318,836346,898158.5,682451,980847,1027750,1031931,1031184,1031013.5,1031931,1031931,1031931]
["WDR35","Short_rib_polydactyly_syndrome_5","intronic","2:20182313:A:T",91.95,98.06,90.525,91.87,96.53,90.07,948957.5,1011130.5,933443,947981,996158.5,929521.5,"2:20159241:G:A",5.3,55.66,54.38,43.38,74.95,19.28,54638.5,573931,560385.5,447698.5,773433,198956.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["DYSF","Limb-girdle_muscular_dystrophy,_type_2B","intronic","2:71900503:C:T",98.345,45.84,50.17,52.94,51.66,97.25,1014877,472710.5,517048.5,546313,533247,1003586,"2:71801297:G:A",97.83,28.23,32.62,34.77,60.02,72.35,1009530.5,290989.5,336246,358738.5,619180,746887,1031931,1031184,1031013.5,1031931,1031931,1031931]
["SLC40A1","Hemochromatosis_type_4","UTR5","2:190445391:T:G",95.83,99.96,89.92,99.96,99.77,99.72,989030.5,1030815.5,927100.5,1031540.5,1029574.5,1029051,"2:190445194:G:C",88.08,100,98.18,98.23,99.64,99.72,909097,1031184,1012215,1013663.5,1028211,1029049,1031931,1031184,1031013.5,1031931,1031931,1031931]
["TMEM237","Joubert_syndrome_14","intronic","2:202504987:G:A",98.77,100,100,100,99.41,97.59,1019271.5,1031184,1031013.5,1031931,1025829,1007101.5,"2:202497155:C:T",73.26,79.25,16.7,74.745,87.925,68.895,756108,817293.5,172221,771614.5,907433.5,711179.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["COL4A4","not_provided","intronic","2:227890527:C:A",99.7,100,94.94,100,99.93,99.33,1028805.5,1031184,978931,1031928.5,1031244,1025060,"2:227883681:A:C",31.83,75.55,57.5,24.61,67.945,75.29,328488,779090.5,592721.5,254047,700954,777093.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["COL6A1","Bethlem_myopathy_1","intronic","21:47409881:C:T",70.91,24.58,47.89,19.56,66.98,28.96,731794,253409.5,493557,201784,691068,298755.5,"21:47416324:C:T",0.04,76.15,61.725,84.23,94.38,36.56,366,785343.5,636324,869333.5,974049.5,377308.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["GCK","Diabetes, MODY","UTR5","7:44229009:G:A",80.57,78.29,69.49,92.23,90.45,90.17,831580,807366,716216.5,951723,933557,930502.5,"7:44228636:G:C",93.32,92.29,99.48,84.26,70.63,97.5,963034.5,951632.5,1025645,869663.5,728831.5,1006258.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["CFTR","Cystic_fibrosis","intronic","7:117229530:G:T",76.59,73.6,71.24,26.3,77.53,43.49,790544,759038,734262.5,271346.5,800169,448867.5,"7:117138947:A:G",64.92,45,71.17,31.89,7.8,35.95,669911.5,464003.5,733550,329067.5,80400,370966,1031931,1031184,1031013.5,1031931,1031931,1031931]
["CFTR","Inborn_genetic_diseases|Cystic_fibrosis","intronic","7:117267864:A:G",97.65,97.35,96.75,98.51,97.5,98.54,1007727,1003759,997518,1016522,1006092.5,1016852,"7:117223764:G:A",41.83,5.9,71.17,1.02,7.8,26.85,431608,60822,733550,10489.5,80400,276940.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["GATA4","Congenital_heart_disease","intronic","8:11612500:T:C",75.33,72.54,75.66,48.6,56.39,41.83,777503,748093,779847.5,501530,581725,431802.5,"8:11614305:A:T",70.98,90.67,99.87,18.04,59.04,69.87,732475,935044,1029692.5,186189,609045,721125.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["GATA4","Congenital_heart_disease","intronic","8:11614418:G:A",87.66,94.13,82.49,65.12,66.98,75.465,904731,970617.5,850426,672158,691068,778866,"8:11562180:G:A",98.31,96.21,94.21,93.82,96.22,88.53,1014485.5,992006.5,971499.5,968224.5,992910.5,913639,1031931,1031184,1031013.5,1031931,1031931,1031931]
["GATA4","Congenital_heart_disease","UTR3","8:11617152:T:C",82.1,83.65,88.66,67.83,89.505,79.755,847403.5,862659,914198,700223,923758,823225,"8:11616410:C:T",77.55,27.66,64.96,30.695,57.51,30.06,800363.5,285162,669837.5,316803.5,593297.5,310171.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["GRHL2","Posterior polymorphous corneal dystrophy 4","intronic","8:102505561:G:T",96.91,96,79.3,95.89,99.41,99.91,1000107,989817,817531.5,989529.5,1025829,1030959,"8:102601928:G:T",39.535,54.24,23.275,13.77,17.07,20.52,407893,559312,239854.5,142111,176213,211758,1031931,1031184,1031013.5,1031931,1031931,1031931]
["EXOSC3","not_provided","intronic","9:37782146:T:C",88.84,91.96,96,97.41,98.92,96.13,916888,948257,989869,1005105,1020705,992023.5,"9:37782925:G:A",92.71,83.535,99.55,83.78,64.54,77.03,956805.5,861531.5,1026373.5,864702,665901,795134.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["CDK5RAP2","Primary_autosomal_recessive_microcephaly_3","intronic","9:123182253:T:C",99.67,95.2,97.82,98.03,96.34,98.68,1028526,981584.5,1008456,1011618,994224,1018289,"9:123282658:T:G",36.74,17.22,79.64,66.78,27.82,14.065,379147,177539.5,821245,689313,287113.5,145128.5,1031931,1031184,1031013.5,1031931,1031931,1031931]
["COL5A1","Ehlers-Danlos_syndrome,_classic_type","intronic","9:137686903:T:G",98.97,96.46,94.33,98.935,97.72,94.83,1021325.5,994597,972650.5,1020943.5,1008348,978677,"9:137704605:A:T",56.8,31,100,8.59,38,26.45,586100,319694.5,1031013.5,88656,392212,272782,1031931,1031184,1031013.5,1031931,1031931,1031931]