ref_additional.gff
ref_additional.gff is a GFF3 file that contains information about:
- duplicated reference regions
- repeated reference regions involved in duplications, tandem duplications, collapsed repeats, and tandem collapsed repeat
- reference regions corresponding to the query overlapped regions in relocations and translocation with overlap differences
- unmapped reference regions not involved in deletion differences
An example of the ref_additional.gff file and a detailed description of the information, provided for repeated regions and regions involved in overlaps, can be found at the wiki page of a difference.
An example with the duplicated reference region entries in the ref_additional.gff file:
##gff-version 3
##sequence-region ref_1 1 296114
ref_1 NucDiff_v2.0 SO:0000001 53630 53661 . . . ID=Region_1;Name=Ref_duplication;duplic_len=32;color=#4005BF
ref_1 NucDiff_v2.0 SO:0000001 53707 53724 . . . ID=Region_2;Name=Ref_duplication;duplic_len=18;color=#4005BF
The ref_additional.gff file contains the following information for each reference region:
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Ref_seq name | |
| 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 | Pos_st | start position of the duplicated region |
| col 5 | Pos_end | end position of the duplicated region |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "Region_1" | |
| col 9, Name | "Ref_duplication" | |
| col 9, duplic_len | Length(duplicated_region) |
An example with the unmapped reference region entries in ref_struct.gff :
##gff-version 3
##sequence-region ref_1 1 115000
ref_1 NucDiff_v2.0 SO:0000001 501 10999 . . . ID=SV_1;Name=uncovered_region;region_len=10499;color=#990000
The ref_struct.gff file contains the following information:
| 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 | pos_st | start of the unmapped reference region |
| col 5 | pos_end | end of the unmapped reference region |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "SV_1" | |
| col 9, Name | "uncovered_region" | |
| col 9, region_len | Length(unmapped_region) |
IGV visualisation of the ref_additional.gff file:
Figure 1: IGV visualisation of the results output in ref_additional.gff file