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Detailed information for vg1121404664:

Variant ID: vg1121404664 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21404664
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CATTAGTATGTGATTAATTAAGTATTTGCTATTCTTTTAAAAAAATAGATTAATACGATTTTTTTAAGCAACTTTTGTACAGAAACCTTTTTTAAAAAAA[C/T,A]
GAACTGTTTAACCGTTTGAAAAGCGTGCGTGCGGAAAACGAAGCAATGGAGTTTAGAACTTGGAGTTCCAAACATAGCACCCACTAAAATTTAGTCATGT

Reverse complement sequence

ACATGACTAAATTTTAGTGGGTGCTATGTTTGGAACTCCAAGTTCTAAACTCCATTGCTTCGTTTTCCGCACGCACGCTTTTCAAACGGTTAAACAGTTC[G/A,T]
TTTTTTTAAAAAAGGTTTCTGTACAAAAGTTGCTTAAAAAAATCGTATTAATCTATTTTTTTAAAAGAATAGCAAATACTTAATTAATCACATACTAATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.50%	22.70%	0.40%	0.00%	A: 3.39%
All Indica	2759	57.00%	36.60%	0.65%	0.00%	A: 5.73%
All Japonica	1512	96.90%	3.00%	0.00%	0.00%	A: 0.07%
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	61.00%	38.50%	0.00%	0.00%	A: 0.50%
Indica II	465	60.20%	36.60%	1.29%	0.00%	A: 1.94%
Indica III	913	52.70%	37.00%	0.55%	0.00%	A: 9.75%
Indica Intermediate	786	57.30%	34.60%	0.89%	0.00%	A: 7.25%
Temperate Japonica	767	95.70%	4.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.00%	0.00%	A: 0.20%
Japonica Intermediate	241	95.40%	4.60%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	12.20%	1.11%	0.00%	A: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121404664	C -> T	LOC_Os11g36330.1	upstream_gene_variant ; 1020.0bp to feature; MODIFIER	silent_mutation	Average:38.903; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N
vg1121404664	C -> T	LOC_Os11g36320-LOC_Os11g36330	intergenic_region ; MODIFIER	silent_mutation	Average:38.903; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N
vg1121404664	C -> A	LOC_Os11g36330.1	upstream_gene_variant ; 1020.0bp to feature; MODIFIER	silent_mutation	Average:38.903; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N
vg1121404664	C -> A	LOC_Os11g36320-LOC_Os11g36330	intergenic_region ; MODIFIER	silent_mutation	Average:38.903; most accessible tissue: Zhenshan97 young leaf, score: 48.658	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121404664	NA	6.26E-06	mr1644	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
vg1121404664	NA	5.04E-06	mr1758_2	Jap_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