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Detailed information for vg0603214907:

Variant ID: vg0603214907 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 3214907
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCTGGAGCTATGCCAGTGGTCTTCAATGCTACAATTCTGAACGGGATGGGGGTGATTGGTTATGTTAAGGATCCTCCTGTATGGCAGCCCTCTGAGGA[T/C]
GTCGGCAATATTCTTAGTGTTCACTTCACCTACTCAGATGTCATATGGCCTTGGACAGGTTATCTTGCCCTGCACTTACAAGTTAAAGATGAAGGATCTC

Reverse complement sequence

GAGATCCTTCATCTTTAACTTGTAAGTGCAGGGCAAGATAACCTGTCCAAGGCCATATGACATCTGAGTAGGTGAAGTGAACACTAAGAATATTGCCGAC[A/G]
TCCTCAGAGGGCTGCCATACAGGAGGATCCTTAACATAACCAATCACCCCCATCCCGTTCAGAATTGTAGCATTGAAGACCACTGGCATAGCTCCAGCAT

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	98.20%	1.80%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	94.40%	5.60%	0.00%	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	95.60%	4.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	80.90%	19.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0603214907	T -> C	LOC_Os06g06810.1	synonymous_variant ; p.Asp168Asp; LOW	synonymous_codon	Average:67.628; most accessible tissue: Zhenshan97 flower, score: 74.708	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0603214907	3.07E-06	3.07E-06	mr1181_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