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Detailed information for vg0208320880:

Variant ID: vg0208320880 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8320880
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAGAGAGAGAAAGAGATGTGGATAAGGATAAGTTGATGGGGTGCATGGGAAGAGGGTTGGATAAGGTCGATCAGTCTAATCACGGTTTTTAAATTAATC[G/A]
GTACCTATAATTCCCACTCGACAAACGCCTGCCTCCTCCTCCTCCTCCTCTTCGTCCGCCTCCCCTCCCCTCCCCTCCGGACACGGTTGGTGTGCGGTTT

Reverse complement sequence

AAACCGCACACCAACCGTGTCCGGAGGGGAGGGGAGGGGAGGCGGACGAAGAGGAGGAGGAGGAGGAGGCAGGCGTTTGTCGAGTGGGAATTATAGGTAC[C/T]
GATTAATTTAAAAACCGTGATTAGACTGATCGACCTTATCCAACCCTCTTCCCATGCACCCCATCAACTTATCCTTATCCACATCTCTTTCTCTCTCTCC

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	96.30%	2.30%	1.48%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	88.40%	6.90%	4.63%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	81.50%	11.10%	7.43%	0.00%	NA
Tropical Japonica	504	98.00%	1.20%	0.79%	0.00%	NA
Japonica Intermediate	241	90.50%	5.80%	3.73%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0208320880	G -> A	LOC_Os02g14910.1	upstream_gene_variant ; 3011.0bp to feature; MODIFIER	silent_mutation	Average:64.745; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N
vg0208320880	G -> A	LOC_Os02g14900.1	downstream_gene_variant ; 3689.0bp to feature; MODIFIER	silent_mutation	Average:64.745; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N
vg0208320880	G -> A	LOC_Os02g14900-LOC_Os02g14910	intergenic_region ; MODIFIER	silent_mutation	Average:64.745; most accessible tissue: Zhenshan97 panicle, score: 86.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208320880	NA	1.55E-06	mr1531	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
vg0208320880	4.11E-07	NA	mr1841	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