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Detailed information for vg0324081467:

Variant ID: vg0324081467 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24081467
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

GTAGTAATGGGCAAACAGTGTCATTCTTTGTGTCATCCCCTAAATCTCATGGCTTGACATTAAATCAAGTTGCTTTGCAAGAGATCCCAATAGTACGAGA[T/C]
TATCCAGATGTGTTCCCTGAGGATTTGCCAGGTATGCCACCTAAGAGAGACATTGAGTTCCGGATAGACAGTACCTGGGACCAACCCTATCCATAAGAGA

Reverse complement sequence

TCTCTTATGGATAGGGTTGGTCCCAGGTACTGTCTATCCGGAACTCAATGTCTCTCTTAGGTGGCATACCTGGCAAATCCTCAGGGAACACATCTGGATA[A/G]
TCTCGTACTATTGGGATCTCTTGCAAAGCAACTTGATTTAATGTCAAGCCATGAGATTTAGGGGATGACACAAAGAATGACACTGTTTGCCCATTACTAC

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	37.80%	20.70%	31.38%	10.11%	NA
All Indica	2759	6.50%	26.20%	50.56%	16.67%	NA
All Japonica	1512	95.50%	4.00%	0.26%	0.26%	NA
Aus	269	42.80%	39.80%	16.73%	0.74%	NA
Indica I	595	6.20%	13.30%	51.60%	28.91%	NA
Indica II	465	6.20%	16.80%	60.86%	16.13%	NA
Indica III	913	3.30%	44.50%	41.51%	10.73%	NA
Indica Intermediate	786	10.70%	20.50%	54.20%	14.63%	NA
Temperate Japonica	767	98.40%	1.20%	0.00%	0.39%	NA
Tropical Japonica	504	94.60%	5.00%	0.40%	0.00%	NA
Japonica Intermediate	241	88.00%	10.80%	0.83%	0.41%	NA
VI/Aromatic	96	6.20%	72.90%	18.75%	2.08%	NA
Intermediate	90	45.60%	20.00%	23.33%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324081467	T -> C	LOC_Os03g43160.1	synonymous_variant ; p.Asp480Asp; LOW	synonymous_codon	Average:20.113; most accessible tissue: Callus, score: 45.649	N	N	N	N
vg0324081467	T -> DEL	LOC_Os03g43160.1	N	frameshift_variant	Average:20.113; most accessible tissue: Callus, score: 45.649	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324081467	NA	4.93E-06	mr1837	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
vg0324081467	2.17E-06	7.41E-06	mr1105_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
vg0324081467	NA	1.52E-06	mr1275_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