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Detailed information for vg0135984305:

Variant ID: vg0135984305 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35984305
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

GTATTCTTTATAGCTAAGTTGCTTAATAATGTTTGACTAATTTCAGAATACTTGCTATCAAAACCGACCAATCATCGAAAGTAACCAAAATTCGCATTAC[A/G]
ATTCTATCACCTGTTGGTATGTTTCATCTCATGTCAAGGTAAACAAAAAGAGACAAAAGTAATCAAGCAAAGCGACCAGAATCACGCCGGCAAACTGCTG

Reverse complement sequence

CAGCAGTTTGCCGGCGTGATTCTGGTCGCTTTGCTTGATTACTTTTGTCTCTTTTTGTTTACCTTGACATGAGATGAAACATACCAACAGGTGATAGAAT[T/C]
GTAATGCGAATTTTGGTTACTTTCGATGATTGGTCGGTTTTGATAGCAAGTATTCTGAAATTAGTCAAACATTATTAAGCAACTTAGCTATAAAGAATAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.90%	12.10%	0.02%	0.00%	NA
All Indica	2759	79.30%	20.60%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	94.20%	5.80%	0.00%	0.00%	NA
Indica III	913	63.20%	36.80%	0.00%	0.00%	NA
Indica Intermediate	786	75.20%	24.70%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0135984305	A -> G	LOC_Os01g62160.1	3_prime_UTR_variant ; 82.0bp to feature; MODIFIER	silent_mutation	Average:71.965; most accessible tissue: Zhenshan97 flower, score: 85.963	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135984305	NA	5.75E-06	mr1887	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
vg0135984305	NA	1.64E-07	mr1200_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