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Detailed information for vg0808906949:

Variant ID: vg0808906949 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8906949
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGTACTTTCTTGAGCATAGGAATTGTGCATTGTAGGCCAACGCTGCCATTTACTTGTTCTGATTTATTAGTTTCCAAGTGATCCTGTCCTCATTTTCC[A/G]
TGAGATGCACGTTTCGAAAGGCGTGGGGATTCGTGGAGATCAGCCGGGGGGCATTTGGGGGCATGGGCCATAGAAGGCGTTGTCAAGGAGCGGGGAGGGT

Reverse complement sequence

ACCCTCCCCGCTCCTTGACAACGCCTTCTATGGCCCATGCCCCCAAATGCCCCCCGGCTGATCTCCACGAATCCCCACGCCTTTCGAAACGTGCATCTCA[T/C]
GGAAAATGAGGACAGGATCACTTGGAAACTAATAAATCAGAACAAGTAAATGGCAGCGTTGGCCTACAATGCACAATTCCTATGCTCAAGAAAGTACAAT

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	64.50%	32.50%	0.04%	2.92%	NA
All Indica	2759	92.00%	5.30%	0.04%	2.68%	NA
All Japonica	1512	11.40%	88.40%	0.00%	0.20%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	81.30%	18.50%	0.17%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	93.20%	0.80%	0.00%	6.02%	NA
Indica Intermediate	786	94.30%	3.30%	0.00%	2.42%	NA
Temperate Japonica	767	4.20%	95.80%	0.00%	0.00%	NA
Tropical Japonica	504	18.80%	81.20%	0.00%	0.00%	NA
Japonica Intermediate	241	18.70%	80.10%	0.00%	1.24%	NA
VI/Aromatic	96	19.80%	21.90%	1.04%	57.29%	NA
Intermediate	90	66.70%	26.70%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808906949	A -> G	LOC_Os08g14800.1	upstream_gene_variant ; 4878.0bp to feature; MODIFIER	silent_mutation	Average:72.342; most accessible tissue: Zhenshan97 root, score: 81.351	N	N	N	N
vg0808906949	A -> G	LOC_Os08g14810.1	intron_variant ; MODIFIER	silent_mutation	Average:72.342; most accessible tissue: Zhenshan97 root, score: 81.351	N	N	N	N
vg0808906949	A -> DEL	N	N	silent_mutation	Average:72.342; most accessible tissue: Zhenshan97 root, score: 81.351	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808906949	NA	1.85E-14	mr1376	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
vg0808906949	NA	1.85E-14	mr1431	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
vg0808906949	NA	1.23E-17	mr1653	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
vg0808906949	NA	9.37E-27	mr1653_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