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Detailed information for vg0319975449:

Variant ID: vg0319975449 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 19975449
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

GATCTGATCCATGTTACATTGGTCCAGTGTTAAACGATACGTCATCGGCAATCCAGCCGATCGGCTATCGTTTATAGATTTAACTTTGGATTCTTTGTTT[C/T]
TTGTTGGTTGCAGGATCAAACCAACTGGCACGACCTAAACCCGAAAGCAAATCTTTGAACCTGCACTAGAGTAAAGCAAATTTCTCAGGCCAGTGTGTGT

Reverse complement sequence

ACACACACTGGCCTGAGAAATTTGCTTTACTCTAGTGCAGGTTCAAAGATTTGCTTTCGGGTTTAGGTCGTGCCAGTTGGTTTGATCCTGCAACCAACAA[G/A]
AAACAAAGAATCCAAAGTTAAATCTATAAACGATAGCCGATCGGCTGGATTGCCGATGACGTATCGTTTAACACTGGACCAATGTAACATGGATCAGATC

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	52.40%	43.60%	0.30%	3.70%	NA
All Indica	2759	77.80%	21.60%	0.33%	0.33%	NA
All Japonica	1512	1.90%	87.40%	0.13%	10.58%	NA
Aus	269	89.60%	10.40%	0.00%	0.00%	NA
Indica I	595	93.10%	6.70%	0.00%	0.17%	NA
Indica II	465	74.00%	25.80%	0.22%	0.00%	NA
Indica III	913	68.50%	30.70%	0.55%	0.33%	NA
Indica Intermediate	786	79.30%	19.70%	0.38%	0.64%	NA
Temperate Japonica	767	0.30%	99.60%	0.00%	0.13%	NA
Tropical Japonica	504	4.80%	66.70%	0.40%	28.17%	NA
Japonica Intermediate	241	0.80%	92.10%	0.00%	7.05%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	42.20%	47.80%	3.33%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0319975449	C -> T	LOC_Os03g36000.1	upstream_gene_variant ; 2044.0bp to feature; MODIFIER	silent_mutation	Average:42.672; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0319975449	C -> T	LOC_Os03g36020.1	upstream_gene_variant ; 4714.0bp to feature; MODIFIER	silent_mutation	Average:42.672; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0319975449	C -> T	LOC_Os03g36000-LOC_Os03g36020	intergenic_region ; MODIFIER	silent_mutation	Average:42.672; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0319975449	C -> DEL	N	N	silent_mutation	Average:42.672; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0319975449	2.76E-07	NA	mr1439	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
vg0319975449	2.05E-06	9.84E-07	mr1439	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
vg0319975449	NA	5.17E-06	mr1718	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
vg0319975449	NA	6.93E-09	mr1835_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
vg0319975449	NA	1.96E-10	mr1893_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