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Detailed information for vg0133434924:

Variant ID: vg0133434924 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 33434924
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.12, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

AGCATATAATCTACCGATTTGGTCTTCCTCAAACTATTACTACGGATCAAGATTCAATCTTTGTGTCCGATGAGTTTGTTCAGTTTGCCGATAGTGTGGG[C/T]
ATCAAGTTGTTGAATTCTTCACCTTATTATGCACAAGCTAATGGGCAAGCCGAGGCATCTAATAAAAGTTTGATCAAATTGATTAAGCGGAAAATTTCTG

Reverse complement sequence

CAGAAATTTTCCGCTTAATCAATTTGATCAAACTTTTATTAGATGCCTCGGCTTGCCCATTAGCTTGTGCATAATAAGGTGAAGAATTCAACAACTTGAT[G/A]
CCCACACTATCGGCAAACTGAACAAACTCATCGGACACAAAGATTGAATCTTGATCCGTAGTAATAGTTTGAGGAAGACCAAATCGGTAGATTATATGCT

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	53.20%	42.60%	4.04%	0.23%	NA
All Indica	2759	80.10%	12.70%	6.78%	0.40%	NA
All Japonica	1512	0.80%	99.10%	0.13%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	80.80%	9.70%	9.41%	0.00%	NA
Indica II	465	80.20%	9.00%	9.25%	1.51%	NA
Indica III	913	80.60%	15.80%	3.61%	0.00%	NA
Indica Intermediate	786	79.00%	13.50%	7.00%	0.51%	NA
Temperate Japonica	767	0.40%	99.30%	0.26%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	24.40%	73.30%	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
vg0133434924	C -> T	LOC_Os01g57800.1	synonymous_variant ; p.Gly1637Gly; LOW	synonymous_codon	Average:27.331; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0133434924	C -> DEL	LOC_Os01g57800.1	N	frameshift_variant	Average:27.331; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0133434924	2.41E-06	NA	mr1008	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
vg0133434924	NA	5.83E-07	mr1008	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
vg0133434924	2.48E-07	4.66E-100	mr1009	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
vg0133434924	NA	1.20E-07	mr1009	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
vg0133434924	NA	1.76E-10	mr1722	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
vg0133434924	4.01E-07	4.01E-07	mr1872	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
vg0133434924	1.99E-07	NA	mr1008_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
vg0133434924	2.30E-06	1.41E-09	mr1008_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