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Detailed information for vg0335289111:

Variant ID: vg0335289111 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35289111
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.51, G: 0.49, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

TATCCTCCCGGCCAACTCCGTCGTCCAGGACGCGAGGATGGGGGCGGTAGGAGGAGCAGCCACCTCCTGTGGCGAGGATGGGGGCGGGACGGGCAGGGGT[A/G]
GGGACCTTGAGGCGAGGTAGTGACGAATGGGATGGGATCGACAGCATTGGGCTGGTGCCATCCATCGTTGTCGCCATCCATAAGCTCAACTTCCTCTGTC

Reverse complement sequence

GACAGAGGAAGTTGAGCTTATGGATGGCGACAACGATGGATGGCACCAGCCCAATGCTGTCGATCCCATCCCATTCGTCACTACCTCGCCTCAAGGTCCC[T/C]
ACCCCTGCCCGTCCCGCCCCCATCCTCGCCACAGGAGGTGGCTGCTCCTCCTACCGCCCCCATCCTCGCGTCCTGGACGACGGAGTTGGCCGGGAGGATA

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	52.30%	47.30%	0.40%	0.00%	NA
All Indica	2759	78.70%	20.80%	0.47%	0.00%	NA
All Japonica	1512	2.40%	97.50%	0.13%	0.00%	NA
Aus	269	78.80%	20.40%	0.74%	0.00%	NA
Indica I	595	68.10%	30.90%	1.01%	0.00%	NA
Indica II	465	90.80%	8.80%	0.43%	0.00%	NA
Indica III	913	78.60%	21.40%	0.00%	0.00%	NA
Indica Intermediate	786	79.80%	19.60%	0.64%	0.00%	NA
Temperate Japonica	767	1.80%	98.00%	0.13%	0.00%	NA
Tropical Japonica	504	4.40%	95.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	99.60%	0.41%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	52.20%	45.60%	2.22%	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
vg0335289111	A -> G	LOC_Os03g62290.1	missense_variant ; p.Tyr28His; MODERATE	nonsynonymous_codon ; Y28H	Average:74.256; most accessible tissue: Zhenshan97 young leaf, score: 84.814	unknown	unknown	TOLERATED	0.68

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335289111	NA	4.48E-06	mr1910_2	Ind_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