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Detailed information for vg0818744396:

Variant ID: vg0818744396 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18744396
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTCCAAGAACACATCGATATCATTGCCGGGTTGTCTCGGACCTTGGATTAACAAGCACAACATAATATATTTCCTTTTGAAGCACAACCATGGCGGGA[A/G]
GTTATAGTTCGCAATAAGAACTGGCCAAGTGCTGTGAGAACTGCTCATGTCTCCGAAAGGATTCATGCCATCCGTACACAAACATATCCTCATGTTTCTG

Reverse complement sequence

CAGAAACATGAGGATATGTTTGTGTACGGATGGCATGAATCCTTTCGGAGACATGAGCAGTTCTCACAGCACTTGGCCAGTTCTTATTGCGAACTATAAC[T/C]
TCCCGCCATGGTTGTGCTTCAAAAGGAAATATATTATGTTGTGCTTGTTAATCCAAGGTCCGAGACAACCCGGCAATGATATCGATGTGTTCTTGGAGCC

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	44.70%	38.20%	12.91%	4.23%	NA
All Indica	2759	69.50%	10.90%	17.62%	1.96%	NA
All Japonica	1512	1.70%	87.40%	1.19%	9.66%	NA
Aus	269	49.10%	14.50%	36.43%	0.00%	NA
Indica I	595	77.30%	18.30%	3.87%	0.50%	NA
Indica II	465	84.10%	7.50%	7.53%	0.86%	NA
Indica III	913	66.00%	2.80%	30.23%	0.88%	NA
Indica Intermediate	786	58.90%	16.80%	19.34%	4.96%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	3.40%	67.10%	2.78%	26.79%	NA
Japonica Intermediate	241	2.10%	91.70%	1.66%	4.56%	NA
VI/Aromatic	96	7.30%	89.60%	3.12%	0.00%	NA
Intermediate	90	33.30%	61.10%	5.56%	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
vg0818744396	A -> G	LOC_Os08g30450.1	intron_variant ; MODIFIER	silent_mutation	Average:28.098; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0818744396	A -> DEL	N	N	silent_mutation	Average:28.098; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818744396	1.48E-06	NA	mr1410	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
vg0818744396	NA	1.21E-06	mr1781	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
vg0818744396	2.21E-06	NA	mr1410_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
vg0818744396	NA	8.79E-06	mr1870_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