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Detailed information for vg0922403934:

Variant ID: vg0922403934 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22403934
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.63, C: 0.37, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCGCCACGCATACTGAAAAGATTTCACTTGAATTAGATGTTGCGGATTTGAATACAATTGACCAGTCCAAACTGCAAGCAATTCTCAGCTCATCTCTG[T/C]
TGCAAGCACTTGACAAGCTCAGAAGAGAGAAGCTCAACAACTCTGAAGAGGCTGAAGAGGTAAAGATAGCAACTTGACTGTTTCCATGAACTCTGAAGGA

Reverse complement sequence

TCCTTCAGAGTTCATGGAAACAGTCAAGTTGCTATCTTTACCTCTTCAGCCTCTTCAGAGTTGTTGAGCTTCTCTCTTCTGAGCTTGTCAAGTGCTTGCA[A/G]
CAGAGATGAGCTGAGAATTGCTTGCAGTTTGGACTGGTCAATTGTATTCAAATCCGCAACATCTAATTCAAGTGAAATCTTTTCAGTATGCGTGGCGCTG

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	81.30%	18.60%	0.06%	0.00%	NA
All Indica	2759	75.40%	24.50%	0.11%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	32.00%	68.00%	0.00%	0.00%	NA
Indica I	595	54.60%	45.40%	0.00%	0.00%	NA
Indica II	465	93.30%	6.70%	0.00%	0.00%	NA
Indica III	913	80.90%	18.90%	0.11%	0.00%	NA
Indica Intermediate	786	74.00%	25.70%	0.25%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0922403934	T -> C	LOC_Os09g39020.1	synonymous_variant ; p.Leu686Leu; LOW	synonymous_codon	Average:71.956; most accessible tissue: Callus, score: 97.251	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922403934	NA	2.46E-09	mr1097	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
vg0922403934	NA	4.16E-06	mr1130	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
vg0922403934	NA	6.49E-11	mr1222	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
vg0922403934	NA	7.46E-06	mr1252	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
vg0922403934	NA	1.16E-06	mr1397	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
vg0922403934	NA	9.48E-06	mr1569	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
vg0922403934	NA	1.68E-08	mr1607	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
vg0922403934	NA	5.38E-06	mr1731	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
vg0922403934	1.73E-07	NA	mr1865	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
vg0922403934	3.38E-14	4.44E-16	mr1865	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
vg0922403934	NA	7.59E-06	mr1868	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
vg0922403934	NA	3.84E-06	mr1898	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
vg0922403934	NA	4.28E-12	mr1918	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
vg0922403934	NA	5.71E-06	mr1918	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
vg0922403934	9.36E-10	1.09E-11	mr1865_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