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Detailed information for vg0204849020:

Variant ID: vg0204849020 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 4849020
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTCCTAAAAACATCACATCGAATCTTTGGACGTATATATAAAGCATTAAATATAGATAAAAAGAAAAACTAATTGTACAGTTTGCATGTAAATCGC[G/A]
AGACGAATCTTTTGAGCCTAATTAGGTCATGATTAGCCATAAGTGCTACAGTAACCCACATATACTAATAATGGATTAATTAGGCTAAAAAAATTCGTCT

Reverse complement sequence

AGACGAATTTTTTTAGCCTAATTAATCCATTATTAGTATATGTGGGTTACTGTAGCACTTATGGCTAATCATGACCTAATTAGGCTCAAAAGATTCGTCT[C/T]
GCGATTTACATGCAAACTGTACAATTAGTTTTTCTTTTTATCTATATTTAATGCTTTATATATACGTCCAAAGATTCGATGTGATGTTTTTAGGAAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.50%	49.30%	0.17%	0.00%	NA
All Indica	2759	51.10%	48.60%	0.25%	0.00%	NA
All Japonica	1512	37.40%	62.60%	0.07%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	53.10%	46.20%	0.67%	0.00%	NA
Indica II	465	57.60%	42.40%	0.00%	0.00%	NA
Indica III	913	46.00%	53.90%	0.11%	0.00%	NA
Indica Intermediate	786	51.80%	48.00%	0.25%	0.00%	NA
Temperate Japonica	767	6.10%	93.90%	0.00%	0.00%	NA
Tropical Japonica	504	75.20%	24.60%	0.20%	0.00%	NA
Japonica Intermediate	241	57.70%	42.30%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	58.90%	41.10%	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
vg0204849020	G -> A	LOC_Os02g09440.1	upstream_gene_variant ; 1837.0bp to feature; MODIFIER	silent_mutation	Average:41.928; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0204849020	G -> A	LOC_Os02g09450.1	intron_variant ; MODIFIER	silent_mutation	Average:41.928; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0204849020	G -> A	LOC_Os02g09450.3	intron_variant ; MODIFIER	silent_mutation	Average:41.928; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0204849020	7.05E-06	NA	mr1076	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
vg0204849020	NA	2.41E-06	mr1096_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
vg0204849020	NA	4.90E-06	mr1224_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
vg0204849020	NA	1.74E-13	mr1241_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
vg0204849020	NA	1.79E-07	mr1246_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
vg0204849020	NA	1.26E-08	mr1404_2	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
vg0204849020	NA	1.07E-06	mr1620_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