Annotation Column Reference¶

This page summarizes columns that may appear in PyFuse outputs.

Core exon annotation columns¶

• Fusion_id: sequential fusion identifier inside a run
• 5'-3'Gene_Partners: normalized fusion partner gene pair
• Fusion_Position: positional relationship of breakpoints across partners
• Fusion_Annotation: fusion class label from exon context logic
• 5'_Exon_Annotation: 5-prime exon-level annotation (strand|loc|gene|transcript)
• 3'_Exon_Annotation: 3-prime exon-level annotation (strand|loc|gene|transcript)
• 5'co-ordinate: genomic coordinate for 5-prime breakpoint
• 3'co-ordinate: genomic coordinate for 3-prime breakpoint
• Distance_between_breakpoints: same-chromosome genomic distance or NA
• Genome: input genome selected for the run (for example GRCh37, GRCh38)

Frame annotation columns¶

• Frame_5p: computed coding frame state of 5-prime partner
• Frame_3p: computed coding frame state of 3-prime partner
• Frame_Status: fusion-level frame interpretation (for example in-frame/out-of-frame classes)

MANE annotation columns (when MANE resource is available)¶

• 5'_MANE_status: MANE class assignment(s) for 5-prime transcript
• 3'_MANE_status: MANE class assignment(s) for 3-prime transcript
• Gene_function: combined function labels (5p|3p) from MANE resource map

Sequence annotation columns (when --reference is provided)¶

• Fusion_nucleotide_sequence: assembled nucleotide sequence around fusion junction
• Fusion_peptide_sequence: translated peptide sequence from assembled nucleotide sequence

Optional external-resource columns (when GTEx/COSMIC resources are enabled)¶

• Present_in_COSMIC
• Histology
• Present_in_GTEX
• Average_Expression
• Number_of_Tissues_that_contain_fusion
• Tissue_Names

Optional blacklist columns¶

When black_list resource is configured, PyFuse appends all columns from that blacklist table after merge on 5'-3'Gene_Partners.