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Detailed information for vg0514439240:

Variant ID: vg0514439240 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14439240
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TTGATGTCTTAGTTGACAAGATCAAAAAACTTGAGGGAGCCCGGGATGAGGTTGCTAATGCTGCTGCCCTAATTGTTCAAGCGATGTTCTTCAATAACAA[C/T]
GGCCCGAGTGCACTTGATGCTTCTGAAATTTTCGACAAGCTGAGAGTTGCTCCGGATACATATTTCAAGAACATCAAAGAAGCTGGAAGTATGGGAGCAA

Reverse complement sequence

TTGCTCCCATACTTCCAGCTTCTTTGATGTTCTTGAAATATGTATCCGGAGCAACTCTCAGCTTGTCGAAAATTTCAGAAGCATCAAGTGCACTCGGGCC[G/A]
TTGTTATTGAAGAACATCGCTTGAACAATTAGGGCAGCAGCATTAGCAACCTCATCCCGGGCTCCCTCAAGTTTTTTGATCTTGTCAACTAAGACATCAA

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	59.30%	40.70%	0.02%	0.00%	NA
All Indica	2759	90.50%	9.50%	0.04%	0.00%	NA
All Japonica	1512	2.80%	97.20%	0.00%	0.00%	NA
Aus	269	81.40%	18.60%	0.00%	0.00%	NA
Indica I	595	87.10%	12.90%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	90.70%	9.30%	0.00%	0.00%	NA
Indica Intermediate	786	90.10%	9.80%	0.13%	0.00%	NA
Temperate Japonica	767	3.00%	97.00%	0.00%	0.00%	NA
Tropical Japonica	504	3.00%	97.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	45.60%	54.40%	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
vg0514439240	C -> T	LOC_Os05g24950.1	synonymous_variant ; p.Asn655Asn; LOW	synonymous_codon	Average:27.807; most accessible tissue: Zhenshan97 root, score: 43.05	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514439240	3.76E-07	3.76E-07	mr1460	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
vg0514439240	NA	1.02E-17	mr1336_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