The phylogeny of 48 alleles, experimentally verified at 21 kb, and its application to clinical allele detection

Table 1 Predicted alleles at internal nodes of the ERMAP phylogeny

Node	Allele^a	Sequence^b	Posterior probability	Status	GenBank number
Reference	Allele1	ATTGGCACCAGGCCGCCGCCCTGCTTAAGCCCTGGCGTGGTACTCGTCACGGTCCGCCGGGGCCGGATTAAA	1	Observed	KX265235
A	SPA18	------G--------------G--------T-------------T---------------------------	0.235	Predicted	na
B	SPA03	------G--------------G--------T-----------------------------------------	0.792^c	Predicted	na
C	SPA06	------G----------A---G--------T-----------T-T---------------------------	0.444	Predicted	na
B′	SPA03	------G--------------G--------T-----------------------------------------	0.516^c	Predicted	na
D	SPA09	------G----------A---G--------T---A-A-----T-T---------------------------	0.608	Predicted	na
E	SPA04	------G--------------G--------------------------------------------------	0.747	Predicted	na
F	SPA07	------G-------------TG--G--G--T-----------------------------------------	0.626	Predicted	na
G	SPA10	-C----G----------A---G--------T---A-A-----T-T---------------------------	0.594	Predicted	na
H	SPA13	-C----G----------A---G----T---T---A-A-----T-TC--------------------------	0.492	Predicted	na
I	Allele12	---------------------G--------------------------------------------------	0.621	Observed	KX265198
J	Allele18	G-----G---A--------TTG--G--G--T-----------------------------------------	0.674	Observed	KX265204
K	Allele08	------G--------------G-------------T------------------------------------	0.888	Observed	KX265194
L	Allele17	-C----G----------A---G----T---T---A-A---C-T-TC--------------------------	0.634	Observed	KX265203

na not applicable
^aAlleles 1, 8, 12, 17, and 18 are experimentally confirmed alleles as published previously [21]. SPA03—SPA18 are predicted alleles (see Additional file 1: Table S1)
^bThe nucleotides at the 72 SNP positions with variations are shown in 5′ to 3′ orientation (Table S2 in Srivastava et al. [21])
^cThe posterior probabilities differ for SPA03 depending on its position in the phylogenetic tree (see Fig. 1)

ISSN: 1479-5876