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Detailed information for vg0416097313:

Variant ID: vg0416097313 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16097313
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, G: 0.29, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCACATGATGGTCAGACATGGGTCCGAAGAGATATAGAAGGAACAACTGTCGATAACATGGTAACTAATTAAAGGTGAGGTTATGAAGGTTGTTCTCT[G/A]
TCTATCTGTCCATTATCACTGATTTCCTTATATCGTTGATATCCTCACTTGGCGAGCTCTTTATTTTTATGGCAGTAATTTTGGATGGAGATTTACTGGG

Reverse complement sequence

CCCAGTAAATCTCCATCCAAAATTACTGCCATAAAAATAAAGAGCTCGCCAAGTGAGGATATCAACGATATAAGGAAATCAGTGATAATGGACAGATAGA[C/T]
AGAGAACAACCTTCATAACCTCACCTTTAATTAGTTACCATGTTATCGACAGTTGTTCCTTCTATATCTCTTCGGACCCATGTCTGACCATCATGTGCAT

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	78.60%	5.70%	12.76%	2.94%	NA
All Indica	2759	80.00%	5.30%	10.66%	4.06%	NA
All Japonica	1512	90.10%	7.70%	2.12%	0.13%	NA
Aus	269	16.70%	2.20%	78.44%	2.60%	NA
Indica I	595	66.90%	17.60%	14.12%	1.34%	NA
Indica II	465	85.40%	0.40%	6.45%	7.74%	NA
Indica III	913	83.50%	1.30%	10.19%	5.04%	NA
Indica Intermediate	786	82.60%	3.60%	11.07%	2.80%	NA
Temperate Japonica	767	97.50%	0.90%	1.56%	0.00%	NA
Tropical Japonica	504	85.30%	13.10%	1.19%	0.40%	NA
Japonica Intermediate	241	76.30%	17.80%	5.81%	0.00%	NA
VI/Aromatic	96	29.20%	1.00%	52.08%	17.71%	NA
Intermediate	90	80.00%	1.10%	17.78%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0416097313	G -> DEL	N	N	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0416097313	G -> A	LOC_Os04g27230.1	upstream_gene_variant ; 1960.0bp to feature; MODIFIER	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0416097313	G -> A	LOC_Os04g27250.1	upstream_gene_variant ; 2169.0bp to feature; MODIFIER	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0416097313	G -> A	LOC_Os04g27250.2	upstream_gene_variant ; 2137.0bp to feature; MODIFIER	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0416097313	G -> A	LOC_Os04g27250.3	upstream_gene_variant ; 2137.0bp to feature; MODIFIER	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0416097313	G -> A	LOC_Os04g27250.4	upstream_gene_variant ; 2137.0bp to feature; MODIFIER	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0416097313	G -> A	LOC_Os04g27240.1	downstream_gene_variant ; 27.0bp to feature; MODIFIER	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0416097313	G -> A	LOC_Os04g27240-LOC_Os04g27250	intergenic_region ; MODIFIER	silent_mutation	Average:48.691; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416097313	1.24E-06	1.24E-06	mr1193_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