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Detailed information for vg0817979262:

Variant ID: vg0817979262 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17979262
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGACGACCAACGCCTTCATCTTCCAGGAACTCCTCTTCTGGGTTTGGGAAAAAATTGAGCAAGACTGAGTACAACCACCGTACTCAACAAGACACACC[T/C]
ACAAGTGCAGAATAAATGCAAGGGAGTACAAGGGGGTTATAATATAAGGGTTAGGATTTGCAGTAAACAGCATTAAAAGACACTTAGTTGCTCAAAGCTA

Reverse complement sequence

TAGCTTTGAGCAACTAAGTGTCTTTTAATGCTGTTTACTGCAAATCCTAACCCTTATATTATAACCCCCTTGTACTCCCTTGCATTTATTCTGCACTTGT[A/G]
GGTGTGTCTTGTTGAGTACGGTGGTTGTACTCAGTCTTGCTCAATTTTTTCCCAAACCCAGAAGAGGAGTTCCTGGAAGATGAAGGCGTTGGTCGTCGCC

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	23.90%	0.50%	5.69%	69.95%	NA
All Indica	2759	8.40%	0.50%	7.10%	84.05%	NA
All Japonica	1512	56.90%	0.50%	2.25%	40.34%	NA
Aus	269	4.50%	0.70%	8.55%	86.25%	NA
Indica I	595	21.00%	1.00%	4.37%	73.61%	NA
Indica II	465	3.70%	0.90%	5.59%	89.89%	NA
Indica III	913	2.50%	0.00%	7.12%	90.36%	NA
Indica Intermediate	786	8.40%	0.40%	10.05%	81.17%	NA
Temperate Japonica	767	85.30%	0.80%	0.65%	13.30%	NA
Tropical Japonica	504	23.40%	0.00%	4.96%	71.63%	NA
Japonica Intermediate	241	36.90%	0.40%	1.66%	61.00%	NA
VI/Aromatic	96	1.00%	0.00%	8.33%	90.62%	NA
Intermediate	90	26.70%	0.00%	8.89%	64.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817979262	T -> C	LOC_Os08g29300.1	upstream_gene_variant ; 1049.0bp to feature; MODIFIER	silent_mutation	Average:8.193; most accessible tissue: Callus, score: 18.757	N	N	N	N
vg0817979262	T -> C	LOC_Os08g29300-LOC_Os08g29310	intergenic_region ; MODIFIER	silent_mutation	Average:8.193; most accessible tissue: Callus, score: 18.757	N	N	N	N
vg0817979262	T -> DEL	N	N	silent_mutation	Average:8.193; most accessible tissue: Callus, score: 18.757	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817979262	1.41E-06	2.16E-06	mr1834_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