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Format Example 1 (for NCBI Human assembly version 37): RESIDUE BASED COORDINATE SYSTEM (comma separated)
Format Example 2 (for NCBI Human assembly version 37): SPACE BASED COORDINATE SYSTEM (comma separated)
[comma separated: chromosome,coordinate,oientation,alleles,user comment(optional) ]
Please do not use spaces except in the user comments field
SIFT accepts both residue-based and a space-based coordinates for single nucleotide variants.
If there is only one column of coordinates, as shown in Example 1 above, SIFT assumes the coordinate
system is residue-based, if there are two columns, as shown in Example 2 above, SIFT assumes the
coordinate system is space-based.
The space-based coordinate system counts the spaces before and after bases rather than the bases themselves.
Zero always refers to the space before the first base.
The sequence 'ACGT' has coordinates (0,4) and its subsequence 'CG' has coordinates (1,3) as shown in Example 3 below.
The difference between the start and end coordinates gives the sequence length. Misinterpretation of these
coordinates can easily lead to 'off-by-one'. errors. Space-based coordinates become necessary when describing
insertions/deletions and genomic rearrangements.
0 A 1 C 2 G 3 T 4
In a residue based system as described in Example 4 below, each base is assigned a coordinate base on its
absolute position, starting from 1. The sequence 'ACGT' has coordinates (1,4) and its subsequence 'CG' has
1 2 34
Use 1 for positve strand and -1 for negative strand. If orientation is not known, use 1 as default.
Use 'base1/base2' where either base1 or base2 may be the reference allele. SIFT will predict for non-reference