Unaligned beginnings
Unaligned beginning - unaligned bases in the beginning of a query sequence.
Figure 1: Unaligned beginning example
An unaligned beginning difference is output in the query_struct.gff and ref_struct.gff files.
An example with the unaligned beginning entries in query_struct.gff :
##gff-version 3
##sequence-region query_4 1 1065
query_4 NucDiff_v2.0 SO:0000667 1 498 . . . ID=SV_1;Name=unaligned_beginning;ins_len=498;query_dir=1;ref_sequence=ref_1;ref_coord=47573;color=#EE0000
##sequence-region query_5 1 1085
query_5 NucDiff_v2.0 SO:0000667 1 499 . . . ID=SV_2;Name=unaligned_beginning;ins_len=499;query_dir=1;ref_sequence=ref_1;ref_coord=59639;color=#EE0000
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:0000667 | Sequence Ontology accession number corresponding to the "insertion" 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 equal to ID in ref_struct.gff |
| col 9, Name | "unaligned_beginning" | |
| col 9, ins_len | Length(Unaligned_beginning) | |
| col 9, query_dir | "1" or "-1" | -1 if the inserted fragment should be reverse complemented before its insertion to a Ref_seq |
| col 9, ref_sequence | Ref_seq | |
| col 9, ref_coord | Ref_pos |
An example with the unaligned beginning entries in ref_struct.gff :
##gff-version 3
##sequence-region ref_1 1 158063
ref_1 NucDiff_v2.0 SO:0000667 47573 47573 . . . ID=SV_1;Name=unaligned_beginning;ins_len=498;query_dir=1;query_sequence=query_4;query_coord=1-498;color=#EE0000
ref_1 NucDiff_v2.0 SO:0000667 59639 59639 . . . ID=SV_2;Name=unaligned_beginning;ins_len=499;query_dir=1;query_sequence=query_5;query_coord=1-499;color=#EE0000
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:0000667 | Sequence Ontology accession number corresponding to the "insertion" SO term |
| col 4 | Ref_pos | |
| col 5 | Ref_pos | |
| 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 | "unaligned_beginning" | |
| col 9, ins_len | Length(Unaligned_beginning) | |
| col 9, query_dir | "1" or "-1" | -1 if the inserted fragment should be reverse complemented before its insertion to a Ref_seq |
| col 9, query_sequence | Query_seq | |
| col 9, query_coord | Ins_st-Ins_end |