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Detailed information for vg0610634708:

Variant ID: vg0610634708 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10634708
Reference Allele: C	Alternative Allele: T,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTAGCCAGAGTAAGCGTCGAGGAAGCTTAATAGTTCGCATCCGGGTGTCGAATCCACCAGTTGGTCTATTCGAGGGAGAGGAAAGTGATCCTTGGGGCA[C/T,G]
GCCTTGTTGAGGTCTGTGAAGTCGACGCACATTCTCCATTTTCCATTGGCTTTCCGCACCATAACTGGGTTGACGAGCCACTCTGGATGGAGGACTTCTC

Reverse complement sequence

GAGAAGTCCTCCATCCAGAGTGGCTCGTCAACCCAGTTATGGTGCGGAAAGCCAATGGAAAATGGAGAATGTGCGTCGACTTCACAGACCTCAACAAGGC[G/A,C]
TGCCCCAAGGATCACTTTCCTCTCCCTCGAATAGACCAACTGGTGGATTCGACACCCGGATGCGAACTATTAAGCTTCCTCGACGCTTACTCTGGCTACG

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	97.90%	0.30%	0.32%	1.46%	G: 0.02%
All Indica	2759	99.70%	0.20%	0.00%	0.04%	G: 0.04%
All Japonica	1512	94.40%	0.30%	0.86%	4.43%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.00%	0.00%	G: 0.11%
Indica Intermediate	786	99.70%	0.10%	0.00%	0.13%	NA
Temperate Japonica	767	91.10%	0.10%	0.78%	7.95%	NA
Tropical Japonica	504	98.20%	0.40%	1.19%	0.20%	NA
Japonica Intermediate	241	97.10%	0.40%	0.41%	2.07%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0610634708	C -> G	LOC_Os06g18750.1	downstream_gene_variant ; 3486.0bp to feature; MODIFIER	silent_mutation	Average:13.663; most accessible tissue: Callus, score: 33.541	N	N	N	N
vg0610634708	C -> G	LOC_Os06g18750-LOC_Os06g18770	intergenic_region ; MODIFIER	silent_mutation	Average:13.663; most accessible tissue: Callus, score: 33.541	N	N	N	N
vg0610634708	C -> T	LOC_Os06g18750.1	downstream_gene_variant ; 3486.0bp to feature; MODIFIER	silent_mutation	Average:13.663; most accessible tissue: Callus, score: 33.541	N	N	N	N
vg0610634708	C -> T	LOC_Os06g18750-LOC_Os06g18770	intergenic_region ; MODIFIER	silent_mutation	Average:13.663; most accessible tissue: Callus, score: 33.541	N	N	N	N
vg0610634708	C -> DEL	N	N	silent_mutation	Average:13.663; most accessible tissue: Callus, score: 33.541	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610634708	3.66E-06	3.66E-06	mr1848_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