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Detailed information for vg0334854019:

Variant ID: vg0334854019 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34854019
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 27. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCAGAGGTGACGGCATGAATCTGGCGACCCTCAACGGCGTGGAGTGAGACAACACGGATGTGGCGGTGGGCCTTGATAGCAGAGGACTCCAAGGCAAG[T/C]
TAATGGCTGACGGCTCCGTGGAGTGGCCCTCTACAGCGGAGGACCCCGAGGTGGGCCTTGGCGGTGGACCTCGACGGCAGAGGACTCCAATGCAGGCTGA

Reverse complement sequence

TCAGCCTGCATTGGAGTCCTCTGCCGTCGAGGTCCACCGCCAAGGCCCACCTCGGGGTCCTCCGCTGTAGAGGGCCACTCCACGGAGCCGTCAGCCATTA[A/G]
CTTGCCTTGGAGTCCTCTGCTATCAAGGCCCACCGCCACATCCGTGTTGTCTCACTCCACGCCGTTGAGGGTCGCCAGATTCATGCCGTCACCTCTGCCG

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	41.80%	5.70%	0.36%	52.09%	NA
All Indica	2759	11.80%	2.50%	0.51%	85.21%	NA
All Japonica	1512	97.60%	1.50%	0.07%	0.79%	NA
Aus	269	17.50%	60.60%	0.00%	21.93%	NA
Indica I	595	4.20%	0.50%	1.18%	94.12%	NA
Indica II	465	12.30%	2.80%	0.22%	84.73%	NA
Indica III	913	13.90%	1.10%	0.11%	84.88%	NA
Indica Intermediate	786	14.90%	5.30%	0.64%	79.13%	NA
Temperate Japonica	767	99.20%	0.30%	0.13%	0.39%	NA
Tropical Japonica	504	94.80%	3.80%	0.00%	1.39%	NA
Japonica Intermediate	241	98.30%	0.80%	0.00%	0.83%	NA
VI/Aromatic	96	83.30%	11.50%	0.00%	5.21%	NA
Intermediate	90	52.20%	6.70%	2.22%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334854019	T -> C	LOC_Os03g61419.1	synonymous_variant ; p.Leu131Leu; LOW	synonymous_codon	Average:55.468; most accessible tissue: Callus, score: 72.107	N	N	N	N
vg0334854019	T -> DEL	LOC_Os03g61419.1	N	frameshift_variant	Average:55.468; most accessible tissue: Callus, score: 72.107	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334854019	NA	2.28E-06	mr1508	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
vg0334854019	NA	3.22E-06	mr1646	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
vg0334854019	NA	7.10E-07	mr1781	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
vg0334854019	1.11E-07	1.12E-06	mr1748_2	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