CLASS .- Submission category. PROGRAM .- EGASP software ID. DATASET .- Submission ID for a given software submitted predictions file. EVALSET .- Havana annotation set ID. SEQUENCE .- ENCODE sequence ID. SEQLEN .- Sequence length. FACTOR .- Not relevant. NC .- Evaluations at the NUCLEOTIDE LEVEL, projecting CODING EXONS into non-overlapping unique "exonic" segments: NC.NuR : Real Nucleotides NC.NuP : Predicted Nucleotides NC.TP : True Positives NC.TN : True Negatives NC.FP : False Positives NC.FN : False Negatives NC.SN : Sensitivity NC.SP : Specificity NC.AC : Average Correlation NC.CC : Correlation Coefficient NE .- Evaluations at the NUCLEOTIDE LEVEL, projecting EXONS (CDS+UTR) into non-overlapping unique "exonic" segments: NE.NuR : Real Nucleotides NE.NuP : Predicted Nucleotides NE.TP : True Positives NE.TN : True Negatives NE.FP : False Positives NE.FN : False Negatives NE.SN : Sensitivity NE.SP : Specificity NE.AC : Average Correlation NE.CC : Correlation Coefficient EC .- Complete evaluation at EXON LEVEL: EC.ANNeEx : ANNotated Exons (CDS+UTR) EC.PRDeEx : PReDicted Exons EC.FNDeEx : FouND Exons EC.SNeEx : Sensitivity EC.SPeEx : Specificity EC.SNSPeEx : (SeNsitivity + SPecificity) / 2 EC.MEeEx : Missing Exons EC.rMEeEx : Missing Exons ratio EC.WEeEx : Wrong Exons EC.rWEeEx : Wrong Exons ratio EC.ANNeAc : ANNotated Acceptor sites (5' exonic splice sites) EC.PRDeAc : PReDicted Acceptor sites EC.FNDeAc : FouND Acceptor sites EC.SNeAc : Sensitivity EC.SPeAc : Specificity EC.SNSPeAc : (SeNsitivity + SPecificity) / 2 EC.MEeAc : Missing Acceptor sites EC.rMEeAc : Missing Acceptor sites ratio EC.WEeAc : Wrong Acceptor sites EC.rWEeAc : Wrong Acceptor sites ratio EC.ANNeDn : ANNotated Donor sites (3' exonic splice sites) EC.PRDeDn : PReDicted Donor sites EC.FNDeDn : FouND Donor sites EC.SNeDn : Sensitivity EC.SPeDn : Specificity EC.SNSPeDn : (SeNsitivity + SPecificity) / 2 EC.MEeDn : Missing Donor sites EC.rMEeDn : Missing Donor sites ratio EC.WEeDn : Wrong Donor sites EC.rWEeDn : Wrong Donor sites ratio EC.ANNtss : ANNotated Transcription Start Sites (TSS, start coordinate for the first exon in the transcript) EC.PRDtss : PReDicted TSS EC.FNDtss : FouND TSS EC.SNtss : Sensitivity EC.SPtss : Specificity EC.SNSPtss : (SeNsitivity + SPecificity) / 2 EC.MEtss : Missing TSS EC.rMEtss : Missing TSS ratio EC.WEtss : Wrong TSS EC.rWEtss : Wrong TSS ratio EC.ANNtes : ANNotated Transcription End Sites (TES, end coordinate for the last exon in the transcript) EC.PRDtes : PReDicted TES EC.FNDtes : FouND TES EC.SNtes : Sensitivity EC.SPtes : Specificity EC.SNSPtes : (SeNsitivity + SPecificity) / 2 EC.MEtes : Missing TES EC.rMEtes : Missing TES ratio EC.WEtes : Wrong TES EC.rWEtes : Wrong TES ratio EC.ANNeIN : ANNotated Introns (for all Exons (CDS+UTR)) EC.PRDeIN : PReDicted Introns EC.FNDeIN : FouND Introns EC.SNeIN : Sensitivity EC.SPeIN : Specificity EC.SNSPeIN : (SeNsitivity + SPecificity) / 2 EC.MIeIN : Missing Introns EC.rMIeIN : Missing Introns ratio EC.WIeIN : Wrong Introns EC.rWIeIN : Wrong Introns ratio EC.ANNCDS : ANNotated Coding Exons (Referees pointed out that using "CDS" here was misleading, as it stands for, sensu strictu, coding sequence) EC.PRDCDS : PReDicted Coding Exons EC.FNDCDS : FouND Coding Exons EC.SNCDS : Sensitivity EC.SPCDS : Specificity EC.SNSPCDS : (SeNsitivity + SPecificity) / 2 EC.MECDS : Missing Coding Exons EC.rMECDS : Missing Coding Exons ratio EC.WECDS : Wrong Coding Exons EC.rWECDS : Wrong Coding Exons ratio EC.ANNcAc : ANNotated Acceptor sites for Coding Exons (5' exonic splice sites) EC.PRDcAc : PReDicted Acceptor sites EC.FNDcAc : FouND Acceptor sites EC.SNcAc : Sensitivity EC.SPcAc : Specificity EC.SNSPcAc : (SeNsitivity + SPecificity) / 2 EC.MEcAc : Missing Acceptor sites EC.rMEcAc : Missing Acceptor sites ratio EC.WEcAc : Wrong Acceptor sites EC.rWEcAc : Wrong Acceptor sites ratio EC.ANNcDn : ANNotated Donor sites for Coding Exons (3' exonic splice sites) EC.PRDcDn : PReDicted Donor sites EC.FNDcDn : FouND Donor sites EC.SNcDn : Sensitivity EC.SPcDn : Specificity EC.SNSPcDn : (SeNsitivity + SPecificity) / 2 EC.MEcDn : Missing Donor sites EC.rMEcDn : Missing Donor sites ratio EC.WEcDn : Wrong Donor sites EC.rWEcDn : Wrong Donor sites ratio EC.ANNatg : ANNotated Start Codon (ATG, start coordinate for the first coding exon, only if "ATG" was found in the corresponding sequence) EC.PRDatg : PReDicted ATG EC.FNDatg : FouND ATG EC.SNatg : Sensitivity EC.SPatg : Specificity EC.SNSPatg : (SeNsitivity + SPecificity) / 2 EC.MEatg : Missing ATG EC.rMEatg : Missing ATG ratio EC.WEatg : Wrong ATG EC.rWEatg : Wrong ATG ratio EC.ANNstp : ANNotated Stop Codon (STP, end coordinate for the last coding exon in the transcript, only if a stop codon was found in the corresponding sequence) EC.PRDstp : PReDicted STP EC.FNDstp : FouND STP EC.SNstp : Sensitivity EC.SPstp : Specificity EC.SNSPstp : (SeNsitivity + SPecificity) / 2 EC.MEstp : Missing STP EC.rMEstp : Missing STP ratio EC.WEstp : Wrong STP EC.rWEstp : Wrong STP ratio EC.ANNfEx : ANNotated First Coding Exons EC.PRDfEx : PReDicted First Coding Exons EC.FNDfEx : FouND First Coding Exons EC.SNfEx : Sensitivity EC.SPfEx : Specificity EC.SNSPfEx : (SeNsitivity + SPecificity) / 2 EC.MEfEx : Missing First Coding Exons EC.rMEfEx : Missing First Coding Exons ratio EC.WEfEx : Wrong First Coding Exons EC.rWEfEx : Wrong First Coding Exons ratio EC.ANNiEx : ANNotated Internal Coding Exons EC.PRDiEx : PReDicted Internal Coding Exons EC.FNDiEx : FouND Internal Coding Exons EC.SNiEx : Sensitivity EC.SPiEx : Specificity EC.SNSPiEx : (SeNsitivity + SPecificity) / 2 EC.MEiEx : Missing Internal Coding Exons EC.rMEiEx : Missing Internal Coding Exons ratio EC.WEiEx : Wrong Internal Coding Exons EC.rWEiEx : Wrong Internal Coding Exons ratio EC.ANNtEx : ANNotated Terminal Coding Exons EC.PRDtEx : PReDicted Terminal Coding Exons EC.FNDtEx : FouND Terminal Coding Exons EC.SNtEx : Sensitivity EC.SPtEx : Specificity EC.SNSPtEx : (SeNsitivity + SPecificity) / 2 EC.MEtEx : Missing Terminal Coding Exons EC.rMEtEx : Missing Terminal Coding Exons ratio EC.WEtEx : Wrong Terminal Coding Exons EC.rWEtEx : Wrong Terminal Coding Exons ratio EC.ANNsEx : ANNotated Single Coding Exons (for the single coding exon genes) EC.PRDsEx : PReDicted Single Coding Exons EC.FNDsEx : FouND Single Coding Exons EC.SNsEx : Sensitivity EC.SPsEx : Specificity EC.SNSPsEx : (SeNsitivity + SPecificity) / 2 EC.MEsEx : Missing Single Coding Exons EC.rMEsEx : Missing Single Coding Exons ratio EC.WEsEx : Wrong Single Coding Exons EC.rWEsEx : Wrong Single Coding Exons ratio EC.ANNcIN : ANNotated Introns for Coding Exons EC.PRDcIN : PReDicted Introns for Coding Exons EC.FNDcIN : FouND Introns for Coding Exons EC.SNcIN : Sensitivity EC.SPcIN : Specificity EC.SNSPcIN : (SeNsitivity + SPecificity) / 2 EC.MIcIN : Missing Introns for Coding Exons EC.rMIcIN : Missing Introns for Coding Exons ratio EC.WIcIN : Wrong Introns for Coding Exons EC.rWIcIN : Wrong Introns for Coding Exons ratio EC.ANNmIN : ANNotated "Annotated" Introns (those already found in the submitted GTF file) EC.PRDmIN : PReDicted "Annotated" Introns EC.FNDmIN : FouND "Annotated" Introns EC.SNmIN : Sensitivity EC.SPmIN : Specificity EC.SNSPmIN : (SeNsitivity + SPecificity) / 2 EC.MImIN : Missing "Annotated" Coding Exons EC.rMImIN : Missing "Annotated" Coding Exons ratio EC.WImIN : Wrong "Annotated" Coding Exons EC.rWImIN : Wrong "Annotated" Coding Exons ratio EC.ANN_EXONtlen : total length for all annotated exons EC.ANN_CDStlen : total length for all annotated coding exons EC.ANN_ratioUTR : ratio untranslated (UTR) annotated exons versus total annotated-exon length EC.ANN_ratioCDS : ratio coding (CDS) annotated exons versus total annotated-exon length EC.ANN_ERRinANNFEAT : errors found in annotation features EC.ANN_ERRinEXNFEAT : errors found in annotated exon features EC.ANN_ERRinCDSFEAT : errors found in annotated coding exon features EC.PRD_EXONtlen : total length for all predicted exons EC.PRD_CDStlen : total length for all predicted coding exons EC.PRD_ratioUTR : ratio untranslated (UTR) predicted exons versus total predicted-exon length EC.PRD_ratioCDS : ratio coding (CDS) predicted exons versus total predicted-exon length EC.PRD_ERRinANNFEAT : errors found in prediction features EC.PRD_ERRinEXNFEAT : errors found in predicted exon features EC.PRD_ERRinCDSFEAT : errors found in predicted coding exon features EC.ANN_avTRxGN : average Transcript per Gene (annotated features) EC.ANN_avEXONxTR : average Exons per Transcript (annotated features) EC.ANN_avEXONlen : average Exon length (annotated features) EC.ANN_avmRNAlen : average mRNA length (annotated features) EC.ANN_avEXNINTlen : average intron length (all exons) (annotated features) EC.ANN_avCDSxTR : average Coding Exons per Transcript (annotated features) EC.ANN_avCDSlen : average Exon length (annotated features) EC.ANN_avcRNAlen : average CDS length (here CDS with the real CDS meaning) (annotated features) EC.ANN_avCDSINTlen : average intron length (all annotated coding exons) EC.ANN_avANNINTlen : average intron length (all introns already found in the annotation GTF file) EC.PRD_avTRxGN : average Transcript per Gene (predicted features) EC.PRD_avEXONxTR : average Exons per Transcript (predicted features) EC.PRD_avEXONlen : average Exon length (predicted features) EC.PRD_avmRNAlen : average mRNA length (predicted features) EC.PRD_avEXNINTlen : average intron length (all exons) (predicted features) EC.PRD_avCDSxTR : average Coding Exons per Transcript (predicted features) EC.PRD_avCDSlen : average Exon length (predicted features) EC.PRD_avcRNAlen : average CDS length (here CDS with the real CDS meaning) (predicted features) EC.PRD_avCDSINTlen : average intron length (all predicted coding exons) EC.PRD_avANNINTlen : average intron length (all introns already found in the prediction GTF file) GC .- Evaluations at the GENE LEVEL, taking only into account CODING EXONS: GC.ANNg : ANNotated genes GC.PRDg : PReDicted genes GC.FNDg : FouND genes GC.SNg : SeNsitivity at gene level GC.SPg : SPecificity at gene level GC.MG : Missing Genes GC.WG : Wrong Genes GC.ANNge : ANNotated exons in genes GC.PRDge : PReDicted exons in genes GC.FNDge : FouND exons in genes GC.SNe : SeNsitivity at exon level GC.SPe : SPecificity at exon level GC.ME : Missing Exons in genes GC.WE : Wrong Exons in genes GC.ANNgi : ANNotated introns in genes GC.PRDgi : PReDicted introns in genes GC.FNDgi : FouND introns in genes GC.SNi : SeNsitivity at intron level GC.SPi : SPecificity at intron level GC.MI : Missing Introns in genes GC.WI : Wrong Introns in genes GC.ANNgn : ANNotated nucleotides in genes GC.PRDgn : PReDicted nucleotides in genes GC.FNDgn : FouND nucleotides in genes GC.SNn : SeNsitivity at nucleotide level GC.SPn : SPecificity at nucleotide level GC.ANNt : ANNotated transcripts GC.PRDt : PReDicted transcripts GC.FNDt : FouND transcripts GC.SNt : SeNsitivity at transcript level GC.SPt : SPecificity at transcript level GC.MT : Missing Transcripts GC.WT : Wrong Transcripts GC.ANNte : ANNotated exons in transcripts GC.PRDte : PReDicted exons in transcripts GC.FNDte : FouND exons in transcripts GC.SNet : SeNsitivity at exon level GC.SPet : SPecificity at exon level GC.MEt : Missing Exons in transcripts GC.WEt : Wrong Exons in transcripts GC.ANNti : ANNotated introns in transcripts GC.PRDti : PReDicted introns in transcripts GC.FNDti : FouND introns in transcripts GC.SNit : SeNsitivity at intron level GC.SPit : SPecificity at intron level GC.MIt : Missing Introns in transcripts GC.WIt : Wrong Introns in transcripts GC.ANNtn : ANNotated nucleotides in transcripts GC.PRDtn : PReDicted nucleotides in transcripts GC.FNDtn : FouND nucleotides in transcripts GC.SNnt : SeNsitivity at nucleotide level GC.SPnt : SPecificity at nucleotide level GC.AvSNt : Average SeNsitivity per transcript GC.AvSPt : Average SPecificity per transcript GC.AvExactTxG : Average Exact Transcript match per Gene GE .- Evaluations at the GENE LEVEL, taking into account EXONS (CDS+UTR): GE.ANNg : ANNotated genes GE.PRDg : PReDicted genes GE.FNDg : FouND genes GE.SNg : SeNsitivity at gene level GE.SPg : SPecificity at gene level GE.MG : Missing Genes GE.WG : Wrong Genes GE.ANNge : ANNotated exons in genes GE.PRDge : PReDicted exons in genes GE.FNDge : FouND exons in genes GE.SNe : SeNsitivity at exon level GE.SPe : SPecificity at exon level GE.ME : Missing Exons in genes GE.WE : Wrong Exons in genes GE.ANNgi : ANNotated introns in genes GE.PRDgi : PReDicted introns in genes GE.FNDgi : FouND introns in genes GE.SNi : SeNsitivity at intron level GE.SPi : SPecificity at intron level GE.MI : Missing Introns in genes GE.WI : Wrong Introns in genes GE.ANNgn : ANNotated nucleotides in genes GE.PRDgn : PReDicted nucleotides in genes GE.FNDgn : FouND nucleotides in genes GE.SNn : SeNsitivity at nucleotide level GE.SPn : SPecificity at nucleotide level GE.ANNt : ANNotated transcripts GE.PRDt : PReDicted transcripts GE.FNDt : FouND transcripts GE.SNt : SeNsitivity at transcript level GE.SPt : SPecificity at transcript level GE.MT : Missing Transcripts GE.WT : Wrong Transcripts GE.ANNte : ANNotated exons in transcripts GE.PRDte : PReDicted exons in transcripts GE.FNDte : FouND exons in transcripts GE.SNet : SeNsitivity at exon level GE.SPet : SPecificity at exon level GE.MEt : Missing Exons in transcripts GE.WEt : Wrong Exons in transcripts GE.ANNti : ANNotated introns in transcripts GE.PRDti : PReDicted introns in transcripts GE.FNDti : FouND introns in transcripts GE.SNit : SeNsitivity at intron level GE.SPit : SPecificity at intron level GE.MIt : Missing Introns in transcripts GE.WIt : Wrong Introns in transcripts GE.ANNtn : ANNotated nucleotides in transcripts GE.PRDtn : PReDicted nucleotides in transcripts GE.FNDtn : FouND nucleotides in transcripts GE.SNnt : SeNsitivity at nucleotide level GE.SPnt : SPecificity at nucleotide level GE.AvSNt : Average SeNsitivity per transcript GE.AvSPt : Average SPecificity per transcript GE.AvExactTxG : Average Exact Transcript match per Gene