geneid docs

geneid eXtended output format (Description)

Gene extracted from a human prediction (geneid eXtended format)

# Gene 7 (Reverse). 3 exons. 476 aa. Score = 47.50 Stop 91832 91834 0.00 - ATAA Terminal 91832 92551 30.56 - 0 0 0.00 3.93 84.26 0.00 AA 237:476 gene_7 Acceptor 92551 92552 3.93 - GCGGTGGTGCGGCTGTCCCCGCAGGTG Donor 93982 93983 1.23 - AAGGTATCT Internal 93983 94263 9.83 - 2 0 1.23 2.79 32.30 0.00 AA 143:236 gene_7 Acceptor 94263 94264 2.79 - AGCTGTGAACTGTTTGTTTGCTAGGGT Donor 95208 95209 2.52 - AAGGTAACC First 95209 95635 7.11 - 0 1 2.52 -1.55 30.08 0.00 AA 1:143 gene_7 Start 95633 95635 -1.55 - TTTAGAAAGCTGAGATGATG >L1084|geneid_v1.1_predicted_protein_7|476_AA MMERIRKEMILMERGLHSPTAGKRFSSLSDSAGGAVLEALENSQHPARLSPRLPSAPLHG ALGDLPAKGKFEIDTLFNLQHPSSESTVSSEIASATESRKKPSHYSEAAAEADMSSDVEV GCSALRSPSGLGAAPLKENNAKGYTESGSVAGTTTSASGSGLGSLHGGGGGGNSGAAALG GSGSGSGADQVRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQ NRRMKDKRQRLAMSWPHPADPSFYTYMMTHAAATGSLPYPFHSHVPLHYYPHVGVTAAAA AAAASGAAAAASSPFATSIRPLDTFRALSHPYSRPELLCSFRHPGLYQAPAAAAGLNSAA SAAAAAAAAAAAASSAAAAGAPPSGSSAPCSCLSCHSSQSAAAAAAAAAAALGSRGGGGS GGGGGGGAGTAGGSDFGCSAAAPRSESGFLPYSAAVLSKTAVSPPDQRDEAPLTR*

Description of columns (geneid eXtended format)
Exon type Type of predicted exon: First, Internal, Terminal or Single
Signal type Type of predicted signal: Acceptor, Donor, Start or Stop codon
Positions Start and finish positions of current exon and signals
Score Score (reliability) of exon and signals
Strand Reading sense: forward or reverse
Frame Left uncomplete codon length in this exon
Remainder Right uncomplete codon length in this exon
Partial scores (exons): Scores (log likelihood) from:

Score for both signals defining exon
Protein coding potential (exon content)
Homology information score (SR regions): provided by user

AA Amino acids corresponding to the exon translation
Key Gene identifier

Description of columns (geneid eXtended format)
Exon type	Type of predicted exon: First, Internal, Terminal or Single
Signal type	Type of predicted signal: Acceptor, Donor, Start or Stop codon
Positions	Start and finish positions of current exon and signals
Score	Score (reliability) of exon and signals
Strand	Reading sense: forward or reverse
Frame	Left uncomplete codon length in this exon
Remainder	Right uncomplete codon length in this exon
Partial scores (exons):	Scores (log likelihood) from: Score for both signals defining exon Protein coding potential (exon content) Homology information score (SR regions): provided by user
AA	Amino acids corresponding to the exon translation
Key	Gene identifier