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Detailed information for vg0334626484:

Variant ID: vg0334626484 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34626484
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGGGAAGCACAGTGGAATATCCAAGTATTAAATCCAATAAAGCAAACATCTGTTTGCTGCCATCTTCTTTTTTAATGCTTCAAGCTGCTACACCTAGA[G/T]
TTCAGGTTTATTGTGTAAACAAAGCAACGGAGTTGTATATCTTGATAAAAATTTGCCAAAACCAGATTACAGCACTTGTGCACGACTCACCTTTTTTTTC

Reverse complement sequence

GAAAAAAAAGGTGAGTCGTGCACAAGTGCTGTAATCTGGTTTTGGCAAATTTTTATCAAGATATACAACTCCGTTGCTTTGTTTACACAATAAACCTGAA[C/A]
TCTAGGTGTAGCAGCTTGAAGCATTAAAAAAGAAGATGGCAGCAAACAGATGTTTGCTTTATTGGATTTAATACTTGGATATTCCACTGTGCTTCCCAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.10%	0.50%	14.73%	31.72%	NA
All Indica	2759	24.30%	0.80%	23.23%	51.69%	NA
All Japonica	1512	99.50%	0.00%	0.20%	0.26%	NA
Aus	269	71.00%	0.40%	12.27%	16.36%	NA
Indica I	595	5.40%	0.70%	15.46%	78.49%	NA
Indica II	465	24.10%	0.00%	18.71%	57.20%	NA
Indica III	913	35.70%	1.40%	30.12%	32.75%	NA
Indica Intermediate	786	25.40%	0.60%	23.79%	50.13%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	94.80%	0.00%	5.21%	0.00%	NA
Intermediate	90	56.70%	0.00%	15.56%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334626484	G -> T	LOC_Os03g60939.1	upstream_gene_variant ; 4261.0bp to feature; MODIFIER	silent_mutation	Average:12.376; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0334626484	G -> T	LOC_Os03g60930.1	downstream_gene_variant ; 1031.0bp to feature; MODIFIER	silent_mutation	Average:12.376; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0334626484	G -> T	LOC_Os03g60930-LOC_Os03g60939	intergenic_region ; MODIFIER	silent_mutation	Average:12.376; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0334626484	G -> DEL	N	N	silent_mutation	Average:12.376; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334626484	NA	1.86E-08	mr1519	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
vg0334626484	NA	6.25E-13	mr1519_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251