query_blocks.gff
qury_blocks.gff is a GFF3 file that contains information about all relocated, translocated, inverted, and reshuffled query regions. In addition, information about all aligned query fragments is provided.
An example of the query_blocks.gff file when the query sequence does not contain any structural differences:
##gff-version 3
##sequence-region query_1 1 400
query_1 NucDiff_v2.0 SO:0000001 1 400 . . . ID=Blk_1;Name=Block;blk_length=400;query_dir=1;ref_sequence=ref_1;ref_coord=1664-2063;color=#00000
In this case the file contains only information about the aligned query fragment that is the whole query sequence.
The query_blocks.gff file contains following information for each aligned region:
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Query_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 | St_q | start of the aligned query fragment |
| col 5 | End_q | end of the aligned query fragment |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "Blk_1" | |
| col 9, Name | "Block" | |
| col 9, blk_length | Length(aligned_query_fragment) | |
| col 9, query_dir | "1" or "-1" | 1 if an aligned query fragment has the same direction as the corresponding reference fragment, otherwise -1 |
| col 9, ref_sequence | Ref_seq_name | |
| col 9, ref_coord | St_r - End_r | start and end of the corresponding reference fragment |
If the query sequence has inversion and/or reshuffling differences, then information about inverted and/or reshuffled regions will be added to the file.
An example of the query_blocks.gff file when the query sequence has inversion and reshuffling differences:
##gff-version 3
##sequence-region query_1 1 3500
query_1 NucDiff_v2.0 SO:0000001 1 500 . . . ID=Blk_1;Name=Block;blk_length=500;query_dir=-1;ref_sequence=ref_1;ref_coord=1501-2000;color=#000000
query_1 NucDiff_v2.0 SO:0000001 1 500 . . . ID=Blk_2;Name=Reshuffling-part_3_gr_0;blk_length=500;query_dir=-1;ref_sequence=ref_1;ref_coord=1501-2000;color=#04B404
query_1 NucDiff_v2.0 SO:0000001 501 1000 . . . ID=Blk_5;Name=Block;blk_length=500;query_dir=-1;ref_sequence=ref_1;ref_coord=501-1000;color=#000000
query_1 NucDiff_v2.0 SO:0000001 501 1000 . . . ID=Blk_6;Name=Inversion;blk_length=500;query_dir=-1;ref_sequence=ref_1;ref_coord=501-1000;color=#DF0101
query_1 NucDiff_v2.0 SO:0000001 501 1000 . . . ID=Blk_7;Name=Reshuffling-part_1_gr_0;blk_length=500;query_dir=-1;ref_sequence=ref_1;ref_coord=501-1000;color=#04B404
...
The query_blocks.gff file contains following information for each inverted/reshuffled region:
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Query_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 | St_q | start of the inverted/reshuffled query region |
| col 5 | End_q | end of the inverted/reshuffled query region |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "Blk_1" | |
| col 9, Name | "Inversion" or "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_length | Length(inv/resh_query_region) | |
| col 9, query_dir | "1" or "-1" | 1 if an inverted/reshuffled query region has the same direction as the corresponding reference region, otherwise -1 |
| col 9, ref_sequence | Ref_seq_name | |
| col 9, ref_coord | St_r - End_r | start and end of the corresponding reference fragment |
If the query sequence has translocation and/or relocation differences, then information about translocated and/or relocated regions will be added to the file.
An example of the query_blocks.gff file when the query sequence has relocation and translocation differences:
##gff-version 3
##sequence-region query_1 1 3500
query_1 NucDiff_v2.0 SO:0000001 1 2500 . . . ID=Blk_1;Name=Block;blk_length=2500;query_dir=-1;ref_sequence=ref_1;ref_coord=1501-4000;color=#000000
query_1 NucDiff_v2.0 SO:0000001 1 2500 . . . ID=Blk_3;Name=Relocation_block;blk_length=2500;color=#01DFD7
query_1 NucDiff_v2.0 SO:0000001 1 3000 . . . ID=Blk_4;Name=Translocation_block;blk_length=3000;color=#0404B4
query_1 NucDiff_v2.0 SO:0000001 2501 3000 . . . ID=Blk_15;Name=Block;blk_length=500;query_dir=1;ref_sequence=ref_1;ref_coord=13501-14000;color=#000000
query_1 NucDiff_v2.0 SO:0000001 2501 3000 . . . ID=Blk_16;Name=Relocation_block;blk_length=500;color=#01DFD7
query_1 NucDiff_v2.0 SO:0000001 3000 3500 . . . ID=Blk_17;Name=Block;blk_length=501;query_dir=1;ref_sequence=ref_2;ref_coord=500-1000;color=#000000
query_1 NucDiff_v2.0 SO:0000001 3000 3500 . . . ID=Blk_18;Name=Translocation_block;blk_length=501;color=#0404B4
The query_blocks.gff file contains the following information for each relocated/translocated region:
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Query_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 | St_q | start of the relocated/translocated query region |
| col 5 | End_q | end of the relocated/translocated query region |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "Blk_1" | |
| col 9, Name | "Relocation_block" or "Translocation_block" | |
| col 9, blk_length | Length(relocated/translocated_query_region) |
IGV visualisation of the query_blocks.gff file:
Figure 1: IGV visualisation of the results output in query_blocks.gff file