Important news regarding SNPs located in multiple chromosomes/positions within assembly.

We were recently warned (thank you Dr. Sechi, Agris , Italy) that SNPs with multiple chromosomes/positions within assembly were not correctly handled in SNPchiMp v.3 (and in previous versions). Some examples (and the new way they're handled) are described below.

Please note that the impact of this change varies according to the species, assembly and chip considered, but in any case, except for two exceptions (PIG and COW) the number of SNPs involved is only ~ 100/200 SNPs).

The way this issue was solved, can be essentially explained with the following examples:

 

Example A: Double entry for the same assembly, but one of the two is missing (rs81391175 in PIG) -  SOLUTION: Only the entry with full information is kept (in this case, chromosome 6, position 114046435)

 

Example B: Double (or more) entries for the same assembly, none of them missing (rs337561410 in PIG) -  SOLUTION: Since we cannot determine which is the correct position, chromosome and position are both set to 99 and 0, respectively.

Example C: More complex examples follow the rules applied above. For example SNP rs137363295 in COW has both "missing" entries and double non-missing entries. In this specific case, chromosome and position on UMD3.1 is set to 99 and 0, respectively, whereas on BTAU4.6, the same values are set to 21 and 3706152.