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Detailed information for vg0317956486:

Variant ID: vg0317956486 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17956486
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGAGCAGTCTCATAAGCAGCAAAAGGATCGACAAACTCCTCATGATCAGAAATATCAGAGACATCCTTGCCTGCTGTAATCCAATCTTCCTTCTGATG[C/T]
CTCTCTAGCTTCTTTACCTTCTTAGCAGTCTTGGCACACATACAAAAGATAGCCCTGAGAGCCTTCTTTATGGGAGAAGAAGACTCAGAACGCTGTGGTG

Reverse complement sequence

CACCACAGCGTTCTGAGTCTTCTTCTCCCATAAAGAAGGCTCTCAGGGCTATCTTTTGTATGTGTGCCAAGACTGCTAAGAAGGTAAAGAAGCTAGAGAG[G/A]
CATCAGAAGGAAGATTGGATTACAGCAGGCAAGGATGTCTCTGATATTTCTGATCATGAGGAGTTTGTCGATCCTTTTGCTGCTTATGAGACTGCTCGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.00%	2.60%	0.40%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	90.90%	8.00%	1.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.50%	2.00%	0.52%	0.00%	NA
Tropical Japonica	504	83.90%	14.50%	1.59%	0.00%	NA
Japonica Intermediate	241	84.20%	13.70%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	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
vg0317956486	C -> T	LOC_Os03g31520.1	synonymous_variant ; p.Arg441Arg; LOW	synonymous_codon	Average:57.936; most accessible tissue: Minghui63 flag leaf, score: 72.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317956486	NA	6.99E-07	mr1040	Jap_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
vg0317956486	1.40E-07	7.08E-10	mr1836_2	Jap_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