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Detailed information for vg1125425266:

Variant ID: vg1125425266 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25425266
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, T: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ACATCGAAGGGCGTGTACACGGAGGACTTCCCCATCCGGCCGCCGCGGCCTTTCAACTACACCAACCGTGATCTCATCCCTCCCGGCCCGCTCGAGGAGG[C/T]
GTTGGAGCCGACGTTCAAGGCGACCAAGCTGAAGCGGTTCAAGTACAACACATCGGTGGAGATCATCTTCCAGAGCACCACGCTGATGCAGAGCGACTCC

Reverse complement sequence

GGAGTCGCTCTGCATCAGCGTGGTGCTCTGGAAGATGATCTCCACCGATGTGTTGTACTTGAACCGCTTCAGCTTGGTCGCCTTGAACGTCGGCTCCAAC[G/A]
CCTCCTCGAGCGGGCCGGGAGGGATGAGATCACGGTTGGTGTAGTTGAAAGGCCGCGGCGGCCGGATGGGGAAGTCCTCCGTGTACACGCCCTTCGATGT

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	83.70%	16.20%	0.04%	0.00%	NA
All Indica	2759	78.30%	21.70%	0.04%	0.00%	NA
All Japonica	1512	90.40%	9.50%	0.07%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	94.60%	5.40%	0.00%	0.00%	NA
Indica II	465	95.30%	4.50%	0.22%	0.00%	NA
Indica III	913	58.60%	41.40%	0.00%	0.00%	NA
Indica Intermediate	786	78.80%	21.20%	0.00%	0.00%	NA
Temperate Japonica	767	99.00%	0.90%	0.13%	0.00%	NA
Tropical Japonica	504	78.20%	21.80%	0.00%	0.00%	NA
Japonica Intermediate	241	88.80%	11.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	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
vg1125425266	C -> T	LOC_Os11g42200.1	missense_variant ; p.Ala449Val; MODERATE	nonsynonymous_codon ; A449V	Average:65.611; most accessible tissue: Zhenshan97 young leaf, score: 85.886	benign	0.404	TOLERATED	0.24

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125425266	NA	5.07E-09	mr1583	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
vg1125425266	3.43E-12	4.78E-14	mr1662	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
vg1125425266	1.24E-07	3.32E-08	mr1662	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
vg1125425266	NA	2.52E-07	mr1696	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
vg1125425266	5.59E-10	1.56E-12	mr1662_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
vg1125425266	NA	2.01E-06	mr1662_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
vg1125425266	8.07E-06	5.89E-06	mr1662_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
vg1125425266	NA	4.05E-07	mr1850_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