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Detailed information for vg0622495472:

Variant ID: vg0622495472 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22495472
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

CGCTTTGCCGGGTTCGGCGATATTAAAACCTCCAAATTCCGCTTGCAAGATTGTGTTTTCGAGGAGAGAAGTTTTTCGGTGGAGCTTTGGAAAATTCCAC[A/G]
TGCCACATATTTCGTCCATTTGAGTTTATTTTTTACATGGTTGGTTCCTGTGAGTTCCTAAGTGTGAAAAAAATATCAAAAAAATAAAATAAAAATAAAA

Reverse complement sequence

TTTTATTTTTATTTTATTTTTTTGATATTTTTTTCACACTTAGGAACTCACAGGAACCAACCATGTAAAAAATAAACTCAAATGGACGAAATATGTGGCA[T/C]
GTGGAATTTTCCAAAGCTCCACCGAAAAACTTCTCTCCTCGAAAACACAATCTTGCAAGCGGAATTTGGAGGTTTTAATATCGCCGAACCCGGCAAAGCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.10%	14.90%	6.98%	36.03%	NA
All Indica	2759	12.80%	24.90%	5.58%	56.65%	NA
All Japonica	1512	95.40%	0.40%	0.46%	3.77%	NA
Aus	269	29.70%	0.00%	52.42%	17.84%	NA
Indica I	595	4.00%	13.30%	5.71%	76.97%	NA
Indica II	465	9.70%	17.60%	4.52%	68.17%	NA
Indica III	913	21.70%	36.80%	6.57%	34.94%	NA
Indica Intermediate	786	11.10%	24.30%	4.96%	59.67%	NA
Temperate Japonica	767	97.70%	0.70%	0.13%	1.56%	NA
Tropical Japonica	504	91.30%	0.20%	0.99%	7.54%	NA
Japonica Intermediate	241	96.70%	0.00%	0.41%	2.90%	NA
VI/Aromatic	96	69.80%	0.00%	23.96%	6.25%	NA
Intermediate	90	53.30%	8.90%	5.56%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622495472	A -> G	LOC_Os06g38040.1	upstream_gene_variant ; 3337.0bp to feature; MODIFIER	silent_mutation	Average:22.7; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0622495472	A -> G	LOC_Os06g38050.1	upstream_gene_variant ; 1121.0bp to feature; MODIFIER	silent_mutation	Average:22.7; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0622495472	A -> G	LOC_Os06g38040-LOC_Os06g38050	intergenic_region ; MODIFIER	silent_mutation	Average:22.7; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0622495472	A -> DEL	N	N	silent_mutation	Average:22.7; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622495472	3.10E-06	2.60E-06	mr1261	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251