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Detailed information for vg0413435802:

Variant ID: vg0413435802 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13435802
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTCTTCGAGACATCTCCAACTGAGAAGAACTTCAACTCTGGTGTAGGGGAAAAGAGAGCAAGACTGAGTACTACCCACTGTACTCAGCAAGTCATACC[G/A]
GAAGAGGAGGTATGATGCAGGATATATCCAAAGGAGGCTAAAGGTCCTTTTGCATAAAGCTAGCATTTAAAAACAGTAGTTGAAAGCAGTAAAACAGTTG

Reverse complement sequence

CAACTGTTTTACTGCTTTCAACTACTGTTTTTAAATGCTAGCTTTATGCAAAAGGACCTTTAGCCTCCTTTGGATATATCCTGCATCATACCTCCTCTTC[C/T]
GGTATGACTTGCTGAGTACAGTGGGTAGTACTCAGTCTTGCTCTCTTTTCCCCTACACCAGAGTTGAAGTTCTTCTCAGTTGGAGATGTCTCGAAGAGGT

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	91.40%	8.60%	0.02%	0.00%	NA
All Indica	2759	94.90%	5.10%	0.04%	0.00%	NA
All Japonica	1512	88.40%	11.60%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	85.00%	15.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	95.40%	4.50%	0.13%	0.00%	NA
Temperate Japonica	767	98.00%	2.00%	0.00%	0.00%	NA
Tropical Japonica	504	80.60%	19.40%	0.00%	0.00%	NA
Japonica Intermediate	241	73.90%	26.10%	0.00%	0.00%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0413435802	G -> A	LOC_Os04g23510.1	upstream_gene_variant ; 3221.0bp to feature; MODIFIER	silent_mutation	Average:65.501; most accessible tissue: Zhenshan97 flag leaf, score: 83.994	N	N	N	N
vg0413435802	G -> A	LOC_Os04g23500.1	intron_variant ; MODIFIER	silent_mutation	Average:65.501; most accessible tissue: Zhenshan97 flag leaf, score: 83.994	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413435802	NA	7.06E-06	mr1278_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
vg0413435802	2.52E-07	NA	mr1350_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
vg0413435802	NA	3.45E-09	mr1350_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
vg0413435802	NA	1.11E-06	mr1397_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
vg0413435802	2.63E-07	NA	mr1730_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
vg0413435802	2.25E-06	9.76E-08	mr1730_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
vg0413435802	NA	7.76E-06	mr1812_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
vg0413435802	1.39E-07	NA	mr1866_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
vg0413435802	NA	7.01E-06	mr1866_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
vg0413435802	3.27E-06	3.27E-06	mr1983_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