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Detailed information for vg1121284164:

Variant ID: vg1121284164 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21284164
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.31, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CACAGCTCAGTCTCAGTGACACGTTGGTCCCACATTCACCCGACTCGACTGTATCAATGTTTCGCTGTTGTGTTTAGTTCACACTGAAGTTTGTAAGTTT[G/A]
GTTGAAATTGGTACGATGTGACAGAAAAGTTGTGTGTGTATGAAAGGTTTGATGTGATGAAAAGTTAGAAGTTTAGAAAAAAAAAAACTTTGGAACTAAA

Reverse complement sequence

TTTAGTTCCAAAGTTTTTTTTTTTCTAAACTTCTAACTTTTCATCACATCAAACCTTTCATACACACACAACTTTTCTGTCACATCGTACCAATTTCAAC[C/T]
AAACTTACAAACTTCAGTGTGAACTAAACACAACAGCGAAACATTGATACAGTCGAGTCGGGTGAATGTGGGACCAACGTGTCACTGAGACTGAGCTGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.40%	8.80%	1.16%	53.58%	NA
All Indica	2759	13.80%	9.00%	1.59%	75.64%	NA
All Japonica	1512	73.20%	10.80%	0.53%	15.48%	NA
Aus	269	46.50%	0.40%	0.74%	52.42%	NA
Indica I	595	29.20%	0.30%	2.02%	68.40%	NA
Indica II	465	7.10%	1.70%	1.94%	89.25%	NA
Indica III	913	9.00%	20.50%	1.10%	69.44%	NA
Indica Intermediate	786	11.60%	6.50%	1.65%	80.28%	NA
Temperate Japonica	767	87.10%	7.00%	0.39%	5.48%	NA
Tropical Japonica	504	62.50%	6.20%	0.60%	30.75%	NA
Japonica Intermediate	241	51.50%	32.40%	0.83%	15.35%	NA
VI/Aromatic	96	64.60%	2.10%	0.00%	33.33%	NA
Intermediate	90	52.20%	4.40%	1.11%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121284164	G -> A	LOC_Os11g36190.1	downstream_gene_variant ; 691.0bp to feature; MODIFIER	silent_mutation	Average:12.453; most accessible tissue: Callus, score: 58.828	N	N	N	N
vg1121284164	G -> A	LOC_Os11g36190.2	downstream_gene_variant ; 691.0bp to feature; MODIFIER	silent_mutation	Average:12.453; most accessible tissue: Callus, score: 58.828	N	N	N	N
vg1121284164	G -> A	LOC_Os11g36180-LOC_Os11g36190	intergenic_region ; MODIFIER	silent_mutation	Average:12.453; most accessible tissue: Callus, score: 58.828	N	N	N	N
vg1121284164	G -> DEL	N	N	silent_mutation	Average:12.453; most accessible tissue: Callus, score: 58.828	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121284164	4.20E-06	4.20E-06	mr1348	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