ref_blocks.gff
ref_blocks.gff is a GFF3 file that contains information about reference regions corresponding to the query regions formed by splitting the query sequences at the points of translocations, relocations, inversions, and reshufflings.
Figure 1: Example of a query sequence split process
An example of the ref_blocks.gff file:
##gff-version 3
##sequence-region ref_1 1 23500
ref_1 NucDiff_v2.0 SO:0000001 1 500 . . . ID=Blk_1;Name=query_1_block;blk_length=500;query_sequence_length=1000;blk_coord_query=1-500;query_dir=1
ref_1 NucDiff_v2.0 SO:0000001 11000 11500 . . . ID=Blk_2;Name=query_1_block;blk_length=501;query_sequence_length=1000;blk_coord_query=500-1000;query_dir=1
ref_1 NucDiff_v2.0 SO:0000001 11501 12002 . . . ID=Blk_3;Name=query_2_block;blk_length=502;query_sequence_length=1000;blk_coord_query=1-502;query_dir=1
ref_1 NucDiff_v2.0 SO:0000001 22501 23000 . . . ID=Blk_4;Name=query_2_block;blk_length=500;query_sequence_length=1000;blk_coord_query=501-1000;query_dir=1
ref_1 NucDiff_v2.0 SO:0000001 23001 23500 . . . ID=Blk_5;Name=query_3_block;blk_length=500;query_sequence_length=1000;blk_coord_query=1-500;query_dir=1
The ref_blocks.gff file contains the following information (see Figure 1 for notations) for each reference region:
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Ref_seq | |
| col 2 | NucDiff_v2.0 | name and current version of the tool |
| col 3 | SO:0000001 | Sequence Ontology accession number corresponding to the "region" SO term |
| col 4 | St_r | |
| col 5 | End_r | |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "Blk_1" | |
| col 9, Name | "<Query_seq_name>_block" | |
| col 9, blk_length | Length(A*) | |
| col 9, query_sequence_length | Length(Query_seq) | |
| col 9, blk_coord_query | St_q - End_q | |
| col 9, query_dir | "1" or "-1" | 1 if the corresponding query region has the same direction as a reference region, otherwise -1 |
IGV visualisation of the ref_blocks.gff file:
Figure 2: IGV visualisation of the results output in ref_blocks.gff file