Reshufflings
reshuffling - an intra-chromosomal structural rearrangement which occurs when several neighbouring reference sequence regions are placed in a different order in a query sequence
Figure 1: Reshuffling example
A reshuffling difference is output in the query_struct.gff and ref_struct.gff files. Information about the reshuffled 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 reshuffling entries in query_struct.gff :
##gff-version 3
##sequence-region query_1 1 1250
query_1 NucDiff_v2.0 SO:0001874 1 250 . . . ID=SV_1;Name=reshuffling-part_3_gr_0;blk_len=250;query_dir=1;ref_sequence=ref_1;ref_coord=501-750;color=#404040
query_1 NucDiff_v2.0 SO:0001874 251 500 . . . ID=SV_2;Name=reshuffling-part_1_gr_0;blk_len=250;query_dir=1;ref_sequence=ref_1;ref_coord=1-250;color=#404040
query_1 NucDiff_v2.0 SO:0001874 501 750 . . . ID=SV_3;Name=reshuffling-part_5_gr_0;blk_len=250;query_dir=1;ref_sequence=ref_1;ref_coord=1001-1250;color=#404040
query_1 NucDiff_v2.0 SO:0001874 751 1000 . . . ID=SV_4;Name=reshuffling-part_2_gr_0;blk_len=250;query_dir=1;ref_sequence=ref_1;ref_coord=251-500;color=#404040
query_1 NucDiff_v2.0 SO:0001874 1001 1250 . . . ID=SV_5;Name=reshuffling-part_4_gr_0;blk_len=250;query_dir=1;ref_sequence=ref_1;ref_coord=751-1000;color=#404040
The query_struct.gff file contains the following information (see Figure 1 for notations) for each reshuffled block:
| 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 | "reshuffling-part_1_gr_0" | part_X - an order number within the reshuffled region, gr_Y- an order number of the reshuffled region |
| col 9, blk_len | Length(1:A) | |
| 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 reshuffling entries in ref_struct.gff :
##gff-version 3
##sequence-region ref_1 1 807680
ref_1 NucDiff_v2.0 SO:0001874 1 250 . . . ID=SV_2;Name=reshuffling-part_1_gr_0;blk_len=250;query_dir=1;query_sequence=query_1;query_coord=251-500;color=#404040
ref_1 NucDiff_v2.0 SO:0001874 251 500 . . . ID=SV_4;Name=reshuffling-part_2_gr_0;blk_len=250;query_dir=1;query_sequence=query_1;query_coord=751-1000;color=#404040
ref_1 NucDiff_v2.0 SO:0001874 501 750 . . . ID=SV_1;Name=reshuffling-part_3_gr_0;blk_len=250;query_dir=1;query_sequence=query_1;query_coord=1-250;color=#404040
ref_1 NucDiff_v2.0 SO:0001874 751 1000 . . . ID=SV_5;Name=reshuffling-part_4_gr_0;blk_len=250;query_dir=1;query_sequence=query_1;query_coord=1001-1250;color=#404040
ref_1 NucDiff_v2.0 SO:0001874 1001 1250 . . . ID=SV_3;Name=reshuffling-part_5_gr_0;blk_len=250;query_dir=1;query_sequence=query_1;query_coord=501-750;color=#404040
The ref_struct.gff file contains the following information (see Figure 1 for notations) for each reshuffled block:
| 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 | "reshuffling-part_1_gr_0" | part_X - order number within reshuffled region, gr_Y- order number of reshuffled region |
| col 9, blk_len | Length(1:A) | |
| 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 |