Relocations with insertion
Relocation - a group of different types of intra-chromosomal structural rearrangements which occur when two regions located in different parts of the same reference sequence are placed nearby in the same query sequence
Relocation with insertion - a relocation where two query fragments have a stretch of bases (not N's) inserted between them, not mapped anywhere on the reference genome. The inserted region is treated as a simple insertion difference.
Figure 1: Relocation with insertion example. The reference coordinates End_r_1 and St_r_2, corresponding to the end of the query relocated block A and to the start of the query relocated block B (End_q_1 and St_q_2, respectively), coincide with the end of the reference relocated block A* and with the start of the reference relocated block B* (Rel_end_r_1 and Rel_st_r_2).
Figure 2: Relocation with insertion example. The reference coordinates End_r_1 and St_r_2, corresponding to the end of the query relocated block A and to the start of the query relocated block B (End_q_1 and St_q_2, respectively), do not coincide with the end of the reference relocated block A* and with the start of the reference relocated block B* (Rel_end_r_1 and Rel_st_r_2).
A relocation with insertion difference is output in the query_struct.gff and ref_struct.gff files. Information about the relocated 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 relocation with insertion entries in query_struct.gff :
##gff-version 3
##sequence-region query_3 1 1050
query_3 NucDiff_v2.0 SO:0001874 501 550 . . . ID=SV_1;Name=relocation-insertion;ins_len=50;ref_sequence=ref_1;blk_1_query=1-500;blk_1_ref=23001-23500;blk_1_query_len=500;blk_1_ref_len=500;blk_1_st_query=1;blk_1_st_ref=23001;blk_1_end_query=500;blk_1_end_ref=23500;blk_2_query=551-1050;blk_2_ref=34001-34500;blk_2_query_len=500;blk_2_ref_len=500;blk_2_st_query=551;blk_2_st_ref=34001;blk_2_end_query=1050;blk_2_end_ref=34500;color=#990099
##sequence-region query_12 1 1350
query_12 NucDiff_v2.0 SO:0001874 501 850 . . . ID=SV_2;Name=relocation-insertion;ins_len=350;ref_sequence=ref_1;blk_1_query=1-500;blk_1_ref=126501-127000;blk_1_query_len=500;blk_1_ref_len=500;blk_1_st_query=1;blk_1_st_ref=126501;blk_1_end_query=500;blk_1_end_ref=127000;blk_2_query=851-1350;blk_2_ref=137501-138000;blk_2_query_len=500;blk_2_ref_len=500;blk_2_st_query=851;blk_2_st_ref=137501;blk_2_end_query=1350;blk_2_end_ref=138000;color=#990099
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 | Ins_st | |
| col 5 | Ins_end | |
| col 6/col 7/col8 | . | score/strand/phase fields are not used |
| col 9, ID | "SV_1" | ID in query_struct.gff is related to ID in ref_struct.gff |
| col 9, Name | "relocation-insertion" | |
| col 9, ins_len | Length(Ins) | |
| col 9, ref_sequence | Ref_seq | |
| col 9, blk_1_query | St_q_1 - End_q_1 | |
| col 9, blk_1_ref | Rel_st_r_1 - Rel_end_r_1 | |
| col 9, blk_1_query_len | Length(A) | |
| col 9, blk_1_ref_len | Length(A*) | |
| col 9, blk_1_st_query | St_q_1 | |
| col 9, blk_1_st_ref | St_r_1 | |
| col 9, blk_1_end_query | End_q_1 | |
| col 9, blk_1_end_ref | End_r_1 | |
| col 9, blk_2_query | St_q_2 - End_q_2 | |
| col 9, blk_2_ref | Rel_st_r_2 - Rel_end_r_2 | |
| col 9, blk_2_query_len | Length(B) | |
| col 9, blk_2_ref_len | Length(B*) | |
| col 9, blk_2_st_query | St_q_2 | |
| col 9, blk_2_st_ref | St_r_2 | |
| col 9, blk_2_end_query | End_q_2 | |
| col 9, blk_2_end_ref | End_r_2 |
An example with the relocation with insertion entries in ref_struct.gff :
##gff-version 3
##sequence-region ref_1 1 149500
ref_1 NucDiff_v2.0 SO:0001874 23500 23500 . . . ID=SV_1.1;Name=relocation-insertion;ins_len=50;query_sequence=query_3;query_coord=500;breakpoint_query=501-550;blk_query=1-500;blk_ref=23001-23500;blk_query_len=500;blk_ref_len=500;color=#990099
ref_1 NucDiff_v2.0 SO:0001874 34001 34001 . . . ID=SV_1.2;Name=relocation-insertion;ins_len=50;query_sequence=query_3;query_coord=551;breakpoint_query=501-550;blk_query=551-1050;blk_ref=34001-34500;blk_query_len=500;blk_ref_len=500;color=#990099
ref_1 NucDiff_v2.0 SO:0001874 127000 127000 . . . ID=SV_2.1;Name=relocation-insertion;ins_len=350;query_sequence=query_12;query_coord=500;breakpoint_query=501-850;blk_query=1-500;blk_ref=126501-127000;blk_query_len=500;blk_ref_len=500;color=#990099
ref_1 NucDiff_v2.0 SO:0001874 137501 137501 . . . ID=SV_2.2;Name=relocation-insertion;ins_len=350;query_sequence=query_12;query_coord=851;breakpoint_query=501-850;blk_query=851-1350;blk_ref=137501-138000;blk_query_len=500;blk_ref_len=500;color=#990099
The ref_struct.gff file contains the following information (see Figure 1 for notations):
| GFF3 fields | Content for Relocation block 1 | Content for Relocation block 2 | Notes |
|---|---|---|---|
| col 1 | Ref_seq | Ref_seq | |
| col 2 | NucDiff_v2.0 | NucDiff_v2.0 | name and current version of the tool |
| col 3 | SO:0001874 | SO:0001874 | Sequence Ontology accession number corresponding to the "intrachromosomal_breakpoint" SO term |
| col 4 | End_r_1 | St_r_2 | |
| col 5 | End_r_1 | St_r_2 | |
| col 6/col 7/col8 | . | . | score/strand/phase fields are not used |
| col 9, ID | "SV_1.1" | "SV_1.2" | ID in ref_struct.gff is related to ID in query_struct.gff |
| col 9, Name | "relocation-insertion" | "relocation-insertion" | |
| col 9, ins_len | Length(Ins) | Length(Ins) | |
| col 9, query_sequence | Query_seq | Query_seq | |
| col 9, query_coord | End_q_1 | St_q_2 | a query_coord base corresponds to the reference base from col 4 |
| col 9, breakpoint_query | Ins_st - Ins_end | Ins_st - Ins_end | |
| col 9, blk_query | St_q_1 - End_q_1 | St_q_2 - End_q_2 | |
| col 9, blk_ref | Rel_st_r_1 - Rel_end_r_1 | Rel_st_r_2 - Rel_end_r_2 | |
| col 9, blk_query_len | Length(A) | Length(B) | |
| col 9, blk_ref_len | Length(A*) | Length(B*) |