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Detailed information for vg1121397365:

Variant ID: vg1121397365 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21397365
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.05, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGACTGTTAATTCTATTTAAGAACTTTTGTATATGCCTTATTAGTTTACCTTAACTTTTAAGAAGGTTTTGATATAAGTTAATTTGTTTACGAAGTAT[A/C]
TATTGTTCTAGTCCAAGTAGTACTACTTACTCCGTTTCAGAATATAAGTTATTCTAGCAATTCCCACGTTCATGTCACTAGAACGGATACTCTCATCTCA

Reverse complement sequence

TGAGATGAGAGTATCCGTTCTAGTGACATGAACGTGGGAATTGCTAGAATAACTTATATTCTGAAACGGAGTAAGTAGTACTACTTGGACTAGAACAATA[T/G]
ATACTTCGTAAACAAATTAACTTATATCAAAACCTTCTTAAAAGTTAAGGTAAACTAATAAGGCATATACAAAAGTTCTTAAATAGAATTAACAGTCGCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.40%	22.20%	0.63%	26.81%	NA
All Indica	2759	50.80%	5.90%	0.98%	42.30%	NA
All Japonica	1512	44.50%	52.40%	0.00%	3.11%	NA
Aus	269	82.20%	9.70%	0.37%	7.81%	NA
Indica I	595	49.40%	18.30%	0.67%	31.60%	NA
Indica II	465	40.00%	1.30%	1.29%	57.42%	NA
Indica III	913	57.50%	1.10%	0.44%	40.96%	NA
Indica Intermediate	786	50.50%	4.80%	1.65%	43.00%	NA
Temperate Japonica	767	31.40%	65.70%	0.00%	2.87%	NA
Tropical Japonica	504	53.00%	43.30%	0.00%	3.77%	NA
Japonica Intermediate	241	68.50%	29.00%	0.00%	2.49%	NA
VI/Aromatic	96	34.40%	42.70%	2.08%	20.83%	NA
Intermediate	90	56.70%	30.00%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121397365	A -> DEL	N	N	silent_mutation	Average:29.961; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg1121397365	A -> C	LOC_Os11g36320-LOC_Os11g36330	intergenic_region ; MODIFIER	silent_mutation	Average:29.961; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121397365	7.00E-07	NA	mr1243	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