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Detailed information for vg0828199395:

Variant ID: vg0828199395 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 28199395
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTATTTTTTTAATTCTGAATTTTTATTATTTCTAATTGTATTTTGTTGACGAAAAAAATCGAACACACCGGCTTGGGAGATCTGCTTAGCTCCTGTGCA[G/A]
GTACAAAGATTGATGAGATGCGGGCTTGCCAGTCAGTTTGATCCTGCAACTGACAAGATATGCAAATAGCAGATCAAAACAGCCGATCGGCTGACAAGCC

Reverse complement sequence

GGCTTGTCAGCCGATCGGCTGTTTTGATCTGCTATTTGCATATCTTGTCAGTTGCAGGATCAAACTGACTGGCAAGCCCGCATCTCATCAATCTTTGTAC[C/T]
TGCACAGGAGCTAAGCAGATCTCCCAAGCCGGTGTGTTCGATTTTTTTCGTCAACAAAATACAATTAGAAATAATAAAAATTCAGAATTAAAAAAATAAG

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	73.70%	6.60%	9.01%	10.69%	NA
All Indica	2759	69.20%	0.10%	13.59%	17.11%	NA
All Japonica	1512	83.50%	13.90%	1.79%	0.79%	NA
Aus	269	88.50%	0.00%	4.83%	6.69%	NA
Indica I	595	41.20%	0.00%	16.30%	42.52%	NA
Indica II	465	61.70%	0.00%	21.94%	16.34%	NA
Indica III	913	91.00%	0.00%	7.12%	1.86%	NA
Indica Intermediate	786	69.50%	0.40%	14.12%	16.03%	NA
Temperate Japonica	767	84.70%	12.40%	1.83%	1.04%	NA
Tropical Japonica	504	90.10%	8.50%	0.99%	0.40%	NA
Japonica Intermediate	241	66.00%	29.90%	3.32%	0.83%	NA
VI/Aromatic	96	9.40%	89.60%	1.04%	0.00%	NA
Intermediate	90	73.30%	12.20%	11.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0828199395	G -> A	LOC_Os08g44900.1	upstream_gene_variant ; 2265.0bp to feature; MODIFIER	silent_mutation	Average:12.767; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0828199395	G -> A	LOC_Os08g44910.1	downstream_gene_variant ; 1629.0bp to feature; MODIFIER	silent_mutation	Average:12.767; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0828199395	G -> A	LOC_Os08g44900-LOC_Os08g44910	intergenic_region ; MODIFIER	silent_mutation	Average:12.767; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N
vg0828199395	G -> DEL	N	N	silent_mutation	Average:12.767; most accessible tissue: Zhenshan97 root, score: 18.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0828199395	NA	9.02E-06	mr1748	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
vg0828199395	NA	6.67E-09	mr1829	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
vg0828199395	NA	7.35E-08	mr1567_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
vg0828199395	NA	1.15E-13	mr1829_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
vg0828199395	NA	1.01E-15	mr1842_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
vg0828199395	NA	2.47E-16	mr1902_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