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Detailed information for vg0134596832:

Variant ID: vg0134596832 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34596832
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.80, G: 0.20, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTATCATCATTAAGAAAGTAACTTAAGATACCTAAATTTGTACTAAAATTTTTGTTACCTCGAGATATACTTAGTACATGAAGATACCAAATTTTAT[A/G]
CTTAAAAAATATGGTACCTCACGTATCTTCTCAATGATGGTAAAACTACCCATCTGAAAATTTGTAGAATCATTTTCAGGATCATCATTGGATGACTTAG

Reverse complement sequence

CTAAGTCATCCAATGATGATCCTGAAAATGATTCTACAAATTTTCAGATGGGTAGTTTTACCATCATTGAGAAGATACGTGAGGTACCATATTTTTTAAG[T/C]
ATAAAATTTGGTATCTTCATGTACTAAGTATATCTCGAGGTAACAAAAATTTTAGTACAAATTTAGGTATCTTAAGTTACTTTCTTAATGATGATAAAAT

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	56.30%	43.60%	0.06%	0.00%	NA
All Indica	2759	84.20%	15.70%	0.04%	0.00%	NA
All Japonica	1512	1.90%	98.00%	0.13%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	93.90%	6.10%	0.00%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	79.10%	20.80%	0.11%	0.00%	NA
Indica Intermediate	786	75.60%	24.40%	0.00%	0.00%	NA
Temperate Japonica	767	1.70%	98.20%	0.13%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	97.90%	0.41%	0.00%	NA
VI/Aromatic	96	7.30%	92.70%	0.00%	0.00%	NA
Intermediate	90	37.80%	62.20%	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
vg0134596832	A -> G	LOC_Os01g59819.1	intron_variant ; MODIFIER	silent_mutation	Average:25.064; most accessible tissue: Callus, score: 43.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134596832	NA	1.52E-06	mr1527	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
vg0134596832	NA	2.06E-14	mr1553	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
vg0134596832	NA	9.98E-16	mr1553_2	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
vg0134596832	NA	5.83E-06	mr1553_2	Ind_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