We just updated HaploGrep2, with the following minor points:
- the Export of the Extended Report (Export / Haplogroup Extendet (txt)) got extended with the “Found_Polys” – see Describtion below:
- The Report for the potential Phantom Mutations got corrected, so that positions with bases according the rCRS reference are not listed anymore.
- Report of the possible Recombinations based now on Hamming Distance instead of Kulczynksi-Distance.
- 6 haplogoups were labeled wrong with H2 instead of H:
|previously until 2.0.3
||correct in 2.1.0
The new column Found_Polys lists the polymorphisms used for the haplogroup classification:
|Sample ID||Range||Haplo group||Cluster||Overall _Rank||Not_ Found Polys||Found _Polys||Remai ning _Polys||AAC _Rem.||Input_ Sample|
|Africa01||16024 -16569; 1-576;||L0f||[L0f, L0f2, L0f2a]||0.9012||73G!||73G 146C 152C 182T! 185A 189G 195C! 207A 247A …||73G 199C 315.1C 16325C 16354T||73G 146C 152C 185A 189G 199C 207A 247A 263G …|
The columns in detail:
SampleID – the identifier of the sample
Range – Sequenced / Genotyped positions on the mitochondrial genome
Haplogroup – resulting Haplogroup
Cluster – if first hit is ambiguous, the result of the cluster is listed in this column
Overall_Rank – the haplogrouping score (from 0.5 to 1) where 0.5 is indicates no SNPs found, and 1 is a perfect match. Now always with “.” as decimal separator
Not_found_Polys – false negatives – mutations expected in this haplogroup but not found
Found_Polys – true positives – mutations found for the resulting haplogroup. Backmutations are considered as well, indicated by ! (see 182T! or 195C! in Sample Africa01)
Remaining_Polys – Variants not being used for this haplogrouping classification – indicates: a) possibly new haplogroup, or b) possible sample admixture, or phantom mutation (false positives). Listed here are hotspot mutations as well as local private mutations (found in at least one different haplogroup) or global private mutation (unknown in the current phylogeny), as well as heteroplasmic mutations or reference identical positions (the latter is often the case for MicroArray based data).
AAC_Remaining – the remaining Variants in the previous column are checked – and marked as such if involved in an Amino Acid Change.
Input_Sample – the profile used for the classification