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Detailed information for vg0209846808:

Variant ID: vg0209846808 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9846808
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GTTAAGCCCTTGGTCAGGATGTCACACAAACCCTCCTCTCCGCAGGGAGCTTGCACCCGCTGCTCGCTTCCCCCTCCTCCTCCTCCTCCCCTGCGCCCCG[C/T]
AGGTGAGGTGAGGCCCCGATCCCACGCGAAGAGCGGCCGATTCCTCCTCTTTGCTTGCGCCATTAACTCCTGTCGGTTTTATGGATTGGTTAACATGAGT

Reverse complement sequence

ACTCATGTTAACCAATCCATAAAACCGACAGGAGTTAATGGCGCAAGCAAAGAGGAGGAATCGGCCGCTCTTCGCGTGGGATCGGGGCCTCACCTCACCT[G/A]
CGGGGCGCAGGGGAGGAGGAGGAGGAGGGGGAAGCGAGCAGCGGGTGCAAGCTCCCTGCGGAGAGGAGGGTTTGTGTGACATCCTGACCAAGGGCTTAAC

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	80.80%	13.40%	4.91%	0.87%	NA
All Indica	2759	69.90%	21.00%	7.68%	1.41%	NA
All Japonica	1512	96.00%	2.80%	1.06%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	57.60%	25.50%	15.29%	1.51%	NA
Indica II	465	58.50%	31.20%	7.96%	2.37%	NA
Indica III	913	90.80%	7.10%	1.42%	0.66%	NA
Indica Intermediate	786	61.70%	27.60%	9.03%	1.65%	NA
Temperate Japonica	767	93.00%	4.70%	2.09%	0.26%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	12.20%	4.44%	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
vg0209846808	C -> T	LOC_Os02g17190.1	upstream_gene_variant ; 1391.0bp to feature; MODIFIER	silent_mutation	Average:67.756; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0209846808	C -> T	LOC_Os02g17180-LOC_Os02g17190	intergenic_region ; MODIFIER	silent_mutation	Average:67.756; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0209846808	C -> DEL	N	N	silent_mutation	Average:67.756; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209846808	NA	1.26E-06	mr1045	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
vg0209846808	NA	2.37E-08	mr1855	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
vg0209846808	9.30E-07	9.30E-07	mr1881	Jap_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
vg0209846808	NA	4.01E-06	mr1317_2	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
vg0209846808	NA	3.22E-07	mr1542_2	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
vg0209846808	NA	1.28E-06	mr1549_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