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Detailed information for vg0402032567:

Variant ID: vg0402032567 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2032567
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCTTGTGTATCTACATTCCGCGAGGAGGTGCAGGGCTGTTCCATGGGTCCGGCGACGTAAGGGGCAGATGGAACCGTTTAGTCAATCTCTTGTCGCTA[G/A]
CCTGTCAGAAGTCCAGACTCTATTTTGGATGATTAGCCAGGCAAAGGTCTTGCACTTACGCAGCGCCCAGGCTTTCCAGTTTAGCCTGTTGAAGTTGGTA

Reverse complement sequence

TACCAACTTCAACAGGCTAAACTGGAAAGCCTGGGCGCTGCGTAAGTGCAAGACCTTTGCCTGGCTAATCATCCAAAATAGAGTCTGGACTTCTGACAGG[C/T]
TAGCGACAAGAGATTGACTAAACGGTTCCATCTGCCCCTTACGTCGCCGGACCCATGGAACAGCCCTGCACCTCCTCGCGGAATGTAGATACACAAGAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.60%	16.20%	0.15%	0.00%	NA
All Indica	2759	83.40%	16.40%	0.25%	0.00%	NA
All Japonica	1512	81.30%	18.70%	0.00%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	87.40%	12.30%	0.34%	0.00%	NA
Indica II	465	94.20%	5.60%	0.22%	0.00%	NA
Indica III	913	72.70%	27.20%	0.11%	0.00%	NA
Indica Intermediate	786	86.30%	13.40%	0.38%	0.00%	NA
Temperate Japonica	767	96.30%	3.70%	0.00%	0.00%	NA
Tropical Japonica	504	60.30%	39.70%	0.00%	0.00%	NA
Japonica Intermediate	241	77.20%	22.80%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0402032567	G -> A	LOC_Os04g04330.1	upstream_gene_variant ; 1883.0bp to feature; MODIFIER	silent_mutation	Average:71.365; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N
vg0402032567	G -> A	LOC_Os04g04330.2	upstream_gene_variant ; 1906.0bp to feature; MODIFIER	silent_mutation	Average:71.365; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N
vg0402032567	G -> A	LOC_Os04g04320-LOC_Os04g04330	intergenic_region ; MODIFIER	silent_mutation	Average:71.365; most accessible tissue: Zhenshan97 panicle, score: 84.374	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402032567	1.46E-06	NA	mr1798	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
vg0402032567	6.97E-11	NA	mr1798_2	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
vg0402032567	2.86E-06	NA	mr1798_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
vg0402032567	3.42E-06	NA	mr1798_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