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Detailed information for vg0210265227:

Variant ID: vg0210265227 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10265227
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTTTTAGCCGGTATTTTGGTACGTCATCTATTTTTGAGTCGGTTTTTAAGATCGTTCGCTTTTGGAAATACATATCCGTGTTTGAGTTGGATTTTAAA[C/T]
TCGTTTGCTTTTGGATATACAAAAGGAGTCATATAAGAATTCTGTTTTAAAAAAACTCTGCATGCTAACTTGAGAAGAAAGTCGGACTCCTAATTGTAGC

Reverse complement sequence

GCTACAATTAGGAGTCCGACTTTCTTCTCAAGTTAGCATGCAGAGTTTTTTTAAAACAGAATTCTTATATGACTCCTTTTGTATATCCAAAAGCAAACGA[G/A]
TTTAAAATCCAACTCAAACACGGATATGTATTTCCAAAAGCGAACGATCTTAAAAACCGACTCAAAAATAGATGACGTACCAAAATACCGGCTAAAACAT

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	46.60%	0.90%	1.46%	51.02%	NA
All Indica	2759	16.60%	1.30%	2.03%	80.10%	NA
All Japonica	1512	98.50%	0.10%	0.07%	1.39%	NA
Aus	269	43.50%	2.60%	4.46%	49.44%	NA
Indica I	595	4.00%	2.70%	3.36%	89.92%	NA
Indica II	465	8.00%	0.90%	1.94%	89.25%	NA
Indica III	913	32.00%	0.90%	0.88%	66.27%	NA
Indica Intermediate	786	13.20%	1.00%	2.42%	83.33%	NA
Temperate Japonica	767	98.80%	0.10%	0.00%	1.04%	NA
Tropical Japonica	504	97.80%	0.00%	0.20%	1.98%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	57.80%	0.00%	0.00%	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
vg0210265227	C -> T	LOC_Os02g17760.1	intron_variant ; MODIFIER	silent_mutation	Average:11.312; most accessible tissue: Callus, score: 58.829	N	N	N	N
vg0210265227	C -> DEL	N	N	silent_mutation	Average:11.312; most accessible tissue: Callus, score: 58.829	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210265227	4.51E-06	2.14E-06	mr1186	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
vg0210265227	7.78E-06	4.58E-06	mr1616	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
vg0210265227	4.87E-06	2.26E-06	mr1639	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