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Detailed information for vg0332502161:

Variant ID: vg0332502161 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32502161
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: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTATATATACTCCCTTCATCCTTAAATGTTTGACGCCGTTGACTTTTTTAAATATGTTTGACCGTTTGTCTTATTCAAAAAATTTAAGCAATTATTAATT[C/T,A]
TTTTCCTACCATTTAATTTATTGTTAAATATACTTTTATGTATACATATAGTTTTACATATTTCACAAAAGTTTTTTGAATAAGACGAACGGCCAAACAT

Reverse complement sequence

ATGTTTGGCCGTTCGTCTTATTCAAAAAACTTTTGTGAAATATGTAAAACTATATGTATACATAAAAGTATATTTAACAATAAATTAAATGGTAGGAAAA[G/A,T]
AATTAATAATTGCTTAAATTTTTTGAATAAGACAAACGGTCAAACATATTTAAAAAAGTCAACGGCGTCAAACATTTAAGGATGAAGGGAGTATATATAA

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	91.60%	8.00%	0.34%	0.00%	A: 0.02%
All Indica	2759	86.20%	13.20%	0.54%	0.00%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.60%	9.20%	0.17%	0.00%	NA
Indica II	465	88.00%	11.20%	0.86%	0.00%	NA
Indica III	913	86.30%	13.40%	0.33%	0.00%	NA
Indica Intermediate	786	81.80%	17.30%	0.89%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	0.00%	A: 1.04%
Intermediate	90	90.00%	10.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0332502161	C -> T	LOC_Os03g57020-LOC_Os03g57030	intergenic_region ; MODIFIER	silent_mutation	Average:25.3; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0332502161	C -> A	LOC_Os03g57020-LOC_Os03g57030	intergenic_region ; MODIFIER	silent_mutation	Average:25.3; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332502161	2.40E-07	NA	mr1723	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
vg0332502161	1.49E-07	1.64E-09	mr1723	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
vg0332502161	NA	1.19E-06	mr1734	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
vg0332502161	4.05E-08	NA	mr1723_2	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
vg0332502161	7.96E-08	4.00E-13	mr1723_2	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