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Detailed information for vg0600809385:

Variant ID: vg0600809385 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 809385
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.28, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CACAAGTAGTCTACTGAATTAACTCCAGCAGTATCCGCCTACTGAAAATCAATTTCATTTTATTTTGTAAACAGAATAGTATTTGATGTAATGCCTTGTA[T/C]
ATCAACGCCGTCAGAAATCATCTTGTAGGCAAGCATAGCTGAATCTCCTTAGTGGCAAAAACAAGATCGTTCGTAAGCTCAACCTTTTGCATTGGAAAGC

Reverse complement sequence

GCTTTCCAATGCAAAAGGTTGAGCTTACGAACGATCTTGTTTTTGCCACTAAGGAGATTCAGCTATGCTTGCCTACAAGATGATTTCTGACGGCGTTGAT[A/G]
TACAAGGCATTACATCAAATACTATTCTGTTTACAAAATAAAATGAAATTGATTTTCAGTAGGCGGATACTGCTGGAGTTAATTCAGTAGACTACTTGTG

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	62.80%	37.20%	0.02%	0.00%	NA
All Indica	2759	91.30%	8.60%	0.04%	0.00%	NA
All Japonica	1512	14.90%	85.10%	0.00%	0.00%	NA
Aus	269	64.30%	35.70%	0.00%	0.00%	NA
Indica I	595	99.30%	0.50%	0.17%	0.00%	NA
Indica II	465	81.10%	18.90%	0.00%	0.00%	NA
Indica III	913	92.30%	7.70%	0.00%	0.00%	NA
Indica Intermediate	786	90.20%	9.80%	0.00%	0.00%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	41.70%	58.30%	0.00%	0.00%	NA
Japonica Intermediate	241	5.00%	95.00%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	48.90%	51.10%	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
vg0600809385	T -> C	LOC_Os06g02380.1	downstream_gene_variant ; 1649.0bp to feature; MODIFIER	silent_mutation	Average:53.696; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0600809385	T -> C	LOC_Os06g02380.2	downstream_gene_variant ; 1649.0bp to feature; MODIFIER	silent_mutation	Average:53.696; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0600809385	T -> C	LOC_Os06g02370-LOC_Os06g02380	intergenic_region ; MODIFIER	silent_mutation	Average:53.696; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0600809385	1.06E-06	3.95E-08	mr1425	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