PN_T2T PN40024 v5

Please cite using this website's URL and also our Nature Communications manuscript, Liang et al. 2019 (DOI: 10.1038/s41467-019-09135-8).

Reference genome with variants (SNPs/InDels) from the respective sample.

The ANN field contains 16 pipe-separated sub-fields:

1. Allele (ALT)
2. Annotation/Effect (using Sequence Ontology terms)
3. Putative Impact (HIGH, MODERATE, LOW, MODIFIER)
4. Gene Name
5. Gene ID
6. Feature Type (e.g., transcript)
7. Feature ID (e.g., Transcript ID)
8. Transcript Biotype
9. Rank/Total (exon or intron rank)
10. HGVS.c (DNA level notation)
11. HGVS.p (Protein level notation)
12. cDNA position/length
13. CDS position/length
14. Protein position/length
15. Distance to feature
16. Errors/Warnings/Information messages

For furthure information on SnpEff, read the documentation

Multiple annotations occur for several reasons:

• A variant may affect more than one gene.
• Genes can have multiple transcripts, leading to different annotations per transcript.
• A single VCF entry can list multiple alternative alleles (non-biallelic variants).
• Each unique combination of variant, gene, and transcript generates its own annotation.

For furthure information on SnpEff, read the documentation

• HIGH: Disruptive impact, likely causing protein truncation or loss of function (e.g., stop_gained, frameshift_variant)
• MODERATE: Non-disruptive but may change protein effectiveness (e.g., missense_variant, inframe_deletion)
• LOW: Mostly harmless or unlikely to change protein behavior (e.g., synonymous_variant)
• MODIFIER: Non-coding variants or variants in non-coding genes where impact is difficult to predict (e.g., exon_variant, downstream_gene_variant).
• ⚠️ Important: Impact categories are meant to help filtering but cannot predict whether a specific variant causes a phenotype of interest.

For furthure information on SnpEff, read the documentation

Use impact categories as a filtering aid, not definitive predictions. A HIGH impact variant isn't necessarily causative for your phenotype of interest, and a LOW impact variant could still be functionally important. Always validate findings with wet-lab experiments.

For single nucleotide variants in protein-coding transcripts:

• SILENT: Codon remains unchanged
• MISSENSE: Codon changes to a different amino acid
• NONSENSE: Codon changes to a STOP codon.