Inversions
inversion - an intra-chromosomal structural rearrangement which occurs when a query sequence region is the reverse complement of a reference sequence region.
Figure 1: Inversion example
An inversion difference is output in the query_struct.gff and ref_struct.gff files. Information about the inverted blocks is also output in the ref_blocks.gff and query_blocks.gff files. The descriptions and examples of the last two files can be found at their wiki pages.
An example with the inversion entries in query_struct.gff :
##gff-version 3
##sequence-region query_5 1 1100
query_5 NucDiff_v2.0 SO:0001874 501 600 . . . ID=SV_1;Name=inversion;blk_len=100;query_dir=1;ref_sequence=ref_1;ref_coord=4671-4770;color=#404040
##sequence-region query_10 1 1300
query_10 NucDiff_v2.0 SO:0001874 501 800 . . . ID=SV_2;Name=inversion;blk_len=300;query_dir=1;ref_sequence=ref_1;ref_coord=10411-10710;color=#404040
##sequence-region query_11 1 1350
query_11 NucDiff_v2.0 SO:0001874 501 850 . . . ID=SV_3;Name=inversion;blk_len=350;query_dir=1;ref_sequence=ref_1;ref_coord=11711-12060;color=#404040
The query_struct.gff file contains the following information (see Figure 1 for notations):
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Query_seq | |
| col 2 | NucDiff_v2.0 | name and current version of the tool |
| col 3 | SO:0001874 | Sequence Ontology accession number corresponding to the "intrachromosomal_breakpoint" SO term |
| col 4 | St_q | |
| col 5 | End_q | |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "SV_1" | ID in query_struct.gff is equal to ID in ref_struct.gff |
| col 9, Name | "inversion" | |
| col 9, blk_len | Length(Inversion) | |
| col 9, query_dir | "1" or "-1" | -1 if inserted fragment should be reverse complemented before its insertion to a Ref_seq |
| col 9, ref_sequence | Ref_seq | |
| col 9, ref_coord | St_r - End_r |
An example with the inversion entries in ref_struct.gff :
##gff-version 3
##sequence-region ref_1 1 13960
ref_1 NucDiff_v2.0 SO:0001874 4671 4770 . . . ID=SV_1;Name=inversion;blk_len=100;query_dir=1;query_sequence=query_5;query_coord=501-600;color=#01DFD7
ref_1 NucDiff_v2.0 SO:0001874 10411 10710 . . . ID=SV_2;Name=inversion;blk_len=300;query_dir=1;query_sequence=query_10;query_coord=501-800;color=#01DFD7
ref_1 NucDiff_v2.0 SO:0001874 11711 12060 . . . ID=SV_3;Name=inversion;blk_len=350;query_dir=1;query_sequence=query_11;query_coord=501-850;color=#01DFD7
The ref_struct.gff file contains the following information (see Figure 1 for notations):
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Ref_seq | |
| col 2 | NucDiff_v2.0 | name and current version of the tool |
| col 3 | SO:0001874 | Sequence Ontology accession number corresponding to the "intrachromosomal_breakpoint" 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 | "SV_1" | ID in ref_struct.gff is equal to ID in query_struct.gff |
| col 9, Name | "inversion" | |
| col 9, blk_len | Length(Inversion) | |
| col 9, query_dir | "1" or "-1" | -1 if inserted fragment should be reverse complemented before its insertion to a Ref_seq |
| col 9, query_sequence | Query_seq | |
| col 9, query_coord | St_q - End_q |