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Detailed information for vg0318061429:

Variant ID: vg0318061429 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18061429
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.24, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCCCCCCCATTTTCATTTAGCCAGGTTATCTTTCATTAGAATTACTTTCTTGTGAAGAAACCAAATAAAGACCTTGATCTTTAGTGGAATTTTCAAGT[C/T]
CCACAGAATTCTCTTTTTATCCGAACATTACAGTTCATGATCGTGGCATACATAGATTTGACGGAAAATTGACCATTCTTATGGAGCGACCATACAAAGA

Reverse complement sequence

TCTTTGTATGGTCGCTCCATAAGAATGGTCAATTTTCCGTCAAATCTATGTATGCCACGATCATGAACTGTAATGTTCGGATAAAAAGAGAATTCTGTGG[G/A]
ACTTGAAAATTCCACTAAAGATCAAGGTCTTTATTTGGTTTCTTCACAAGAAAGTAATTCTAATGAAAGATAACCTGGCTAAATGAAAATGGGGGGGGAG

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	68.50%	31.00%	0.02%	0.40%	NA
All Indica	2759	97.60%	2.00%	0.04%	0.43%	NA
All Japonica	1512	14.60%	85.20%	0.00%	0.20%	NA
Aus	269	92.60%	7.40%	0.00%	0.00%	NA
Indica I	595	97.50%	1.50%	0.17%	0.84%	NA
Indica II	465	97.00%	2.60%	0.00%	0.43%	NA
Indica III	913	98.90%	1.00%	0.00%	0.11%	NA
Indica Intermediate	786	96.40%	3.10%	0.00%	0.51%	NA
Temperate Japonica	767	0.40%	99.50%	0.00%	0.13%	NA
Tropical Japonica	504	39.50%	60.10%	0.00%	0.40%	NA
Japonica Intermediate	241	7.90%	92.10%	0.00%	0.00%	NA
VI/Aromatic	96	26.00%	74.00%	0.00%	0.00%	NA
Intermediate	90	57.80%	37.80%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0318061429	C -> T	LOC_Os03g31634.1	downstream_gene_variant ; 200.0bp to feature; MODIFIER	silent_mutation	Average:32.983; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N
vg0318061429	C -> T	LOC_Os03g31634-LOC_Os03g31640	intergenic_region ; MODIFIER	silent_mutation	Average:32.983; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N
vg0318061429	C -> DEL	N	N	silent_mutation	Average:32.983; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318061429	NA	3.87E-06	mr1215	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
vg0318061429	NA	9.20E-08	mr1217	Jap_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
vg0318061429	NA	2.89E-06	mr1583	Jap_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
vg0318061429	1.22E-07	2.52E-12	mr1750	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
vg0318061429	NA	6.51E-06	mr1830	Jap_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
vg0318061429	NA	6.46E-07	mr1845	Jap_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
vg0318061429	NA	1.48E-09	mr1852	Jap_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
vg0318061429	NA	1.52E-08	mr1136_2	Jap_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