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Detailed information for vg0203441067:

Variant ID: vg0203441067 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3441067
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.05, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CGAACAAATACATCATAGAAAGGTGGAGGAAGAAAGACAACAACATAACAGGTCTATTCAGAGGAGAATCAAGTAATGGACCTAATGCTATGCTAATGTA[C/T]
AACGTGCTCTCGCAAAAAATGTCAGAATTAGCATCAAAGGGTTGTAAGAGACCAGAGATATATAGTTACCTGGTTGGAGAAGTGGAGAAGTTGGATAGCA

Reverse complement sequence

TGCTATCCAACTTCTCCACTTCTCCAACCAGGTAACTATATATCTCTGGTCTCTTACAACCCTTTGATGCTAATTCTGACATTTTTTGCGAGAGCACGTT[G/A]
TACATTAGCATAGCATTAGGTCCATTACTTGATTCTCCTCTGAATAGACCTGTTATGTTGTTGTCTTTCTTCCTCCACCTTTCTATGATGTATTTGTTCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.10%	29.20%	0.74%	16.02%	NA
All Indica	2759	88.40%	3.10%	0.80%	7.72%	NA
All Japonica	1512	4.60%	67.90%	0.60%	26.98%	NA
Aus	269	4.50%	84.00%	0.00%	11.52%	NA
Indica I	595	95.00%	2.40%	0.17%	2.52%	NA
Indica II	465	89.50%	1.70%	0.65%	8.17%	NA
Indica III	913	88.60%	2.10%	1.42%	7.89%	NA
Indica Intermediate	786	82.40%	5.70%	0.64%	11.20%	NA
Temperate Japonica	767	3.40%	70.50%	0.78%	25.29%	NA
Tropical Japonica	504	7.30%	63.90%	0.60%	28.17%	NA
Japonica Intermediate	241	2.50%	67.60%	0.00%	29.88%	NA
VI/Aromatic	96	7.30%	7.30%	0.00%	85.42%	NA
Intermediate	90	33.30%	36.70%	4.44%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203441067	C -> T	LOC_Os02g06820.1	synonymous_variant ; p.Tyr254Tyr; LOW	synonymous_codon	Average:27.88; most accessible tissue: Callus, score: 76.15	N	N	N	N
vg0203441067	C -> DEL	LOC_Os02g06820.1	N	frameshift_variant	Average:27.88; most accessible tissue: Callus, score: 76.15	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203441067	NA	2.66E-32	mr1745	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
vg0203441067	9.64E-07	9.64E-07	mr1855	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
vg0203441067	NA	2.98E-11	mr1938	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
vg0203441067	NA	9.70E-06	mr1170_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
vg0203441067	NA	2.19E-41	mr1745_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