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Unaligned sequences
kseniakh edited this page Mar 10, 2017
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unaligned sequence - a query sequence that has no matches of length equal to or longer than a given number of bases with the reference genome.
An unaligned sequence difference is output in the query_struct.gff file.
An example with the unaligned sequence entries in query_struct.gff :
##gff-version 3
##sequence-region query_5 1 65
query_5 NucDiff_v2.0 SO:0000001 1 65 . . . ID=SV_4;Name=unaligned_sequence;color=#990000
##sequence-region query_6 1 85
query_6 NucDiff_v2.0 SO:0000001 1 85 . . . ID=SV_5;Name=unaligned_sequence;color=#990000
The query_struct.gff file contains the following information:
| GFF3 fields | Content | Notes |
|---|---|---|
| col 1 | Query_seq | |
| 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 | Query_seq start | |
| col 5 | Query_seq 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_sequence" |