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Detailed information for vg0321300282:

Variant ID: vg0321300282 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21300282
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTGATCCTATATTGCAAATGTCCTAATGTTTTCTTTCAAATACCGCATTTGTTTTGCAATTATACTATGGGATGGTTACCTATTGTTACAGCTATGC[T/C]
TTTTGGATACCATGCTCCTTTGTTAGCTTGGGTTATAACATGATTAGACTTTGGACTAGGAATTGCTTAGCCATGCTTAGTTCAACTAGCACACAATGGG

Reverse complement sequence

CCCATTGTGTGCTAGTTGAACTAAGCATGGCTAAGCAATTCCTAGTCCAAAGTCTAATCATGTTATAACCCAAGCTAACAAAGGAGCATGGTATCCAAAA[A/G]
GCATAGCTGTAACAATAGGTAACCATCCCATAGTATAATTGCAAAACAAATGCGGTATTTGAAAGAAAACATTAGGACATTTGCAATATAGGATCAATAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.90%	4.90%	15.40%	41.77%	NA
All Indica	2759	5.50%	2.30%	22.65%	69.55%	NA
All Japonica	1512	98.30%	0.10%	0.07%	1.52%	NA
Aus	269	3.70%	61.70%	34.57%	0.00%	NA
Indica I	595	3.70%	0.20%	29.41%	66.72%	NA
Indica II	465	6.50%	5.40%	14.84%	73.33%	NA
Indica III	913	3.60%	0.50%	25.08%	70.76%	NA
Indica Intermediate	786	8.50%	4.10%	19.34%	68.07%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	95.60%	0.00%	0.20%	4.17%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	1.00%	1.04%	2.08%	NA
Intermediate	90	56.70%	1.10%	8.89%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321300282	T -> C	LOC_Os03g38370.1	downstream_gene_variant ; 1707.0bp to feature; MODIFIER	silent_mutation	Average:16.229; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0321300282	T -> C	LOC_Os03g38375.1	downstream_gene_variant ; 3153.0bp to feature; MODIFIER	silent_mutation	Average:16.229; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0321300282	T -> C	LOC_Os03g38359-LOC_Os03g38370	intergenic_region ; MODIFIER	silent_mutation	Average:16.229; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0321300282	T -> DEL	N	N	silent_mutation	Average:16.229; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321300282	1.85E-06	7.01E-09	mr1310	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
vg0321300282	7.98E-07	7.98E-07	mr1926	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