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Detailed information for vg0825603421:

Variant ID: vg0825603421 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25603421
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCAGTGGGTCCCCACTACCCTCCCCTCTCTCTCCCAGATTTGGTCGGAGGTAAGGCAGTCGGTGAGTAGCAGCAGCAGCTCGTCCACGGCGGCTTCAG[C/T]
GGCGCCTCCGCTGGTCCGTCCTCGACTTCCATCACGCCGGCGCTGCCTCCACCCTCTGCCTCCATCGCGCCGCCTCCGCCAGTCCATCCTCAACCTCCAT

Reverse complement sequence

ATGGAGGTTGAGGATGGACTGGCGGAGGCGGCGCGATGGAGGCAGAGGGTGGAGGCAGCGCCGGCGTGATGGAAGTCGAGGACGGACCAGCGGAGGCGCC[G/A]
CTGAAGCCGCCGTGGACGAGCTGCTGCTGCTACTCACCGACTGCCTTACCTCCGACCAAATCTGGGAGAGAGAGGGGAGGGTAGTGGGGACCCACTGCCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.90%	32.80%	0.25%	0.00%	NA
All Indica	2759	78.00%	21.80%	0.25%	0.00%	NA
All Japonica	1512	42.60%	57.20%	0.20%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	61.20%	38.50%	0.34%	0.00%	NA
Indica II	465	87.50%	12.30%	0.22%	0.00%	NA
Indica III	913	80.20%	19.70%	0.11%	0.00%	NA
Indica Intermediate	786	82.40%	17.20%	0.38%	0.00%	NA
Temperate Japonica	767	69.10%	30.60%	0.26%	0.00%	NA
Tropical Japonica	504	5.40%	94.60%	0.00%	0.00%	NA
Japonica Intermediate	241	36.10%	63.50%	0.41%	0.00%	NA
VI/Aromatic	96	38.50%	60.40%	1.04%	0.00%	NA
Intermediate	90	72.20%	26.70%	1.11%	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
vg0825603421	C -> T	LOC_Os08g40470.1	missense_variant ; p.Ala135Val; MODERATE	nonsynonymous_codon ; A135V	Average:71.897; most accessible tissue: Zhenshan97 young leaf, score: 88.878	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825603421	NA	2.07E-06	mr1382	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
vg0825603421	NA	7.13E-08	mr1552	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
vg0825603421	NA	3.40E-06	mr1554	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
vg0825603421	1.48E-08	4.29E-12	mr1874	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
vg0825603421	NA	7.58E-10	mr1388_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
vg0825603421	4.36E-07	2.71E-10	mr1874_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