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Detailed information for vg0818712613:

Variant ID: vg0818712613 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18712613
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, G: 0.06, A: 0.01, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

CTATTTTCTTCATCTTCATGATTGGTGGACTTCGTCATCGTCTTTGATGCGTGTCTATATCTTCACCGTCGGCTTGCTTTCGTCACCACCGACTGGTATC[G/C]
TCGCCTTCACGGATGGCTTATTATGTCGCCACTAGTAGGCATCTTCATCTTCTTCACCAGCTGCCTTGTCTGTCACCGACTAATTATTTCGCTGCCATGG

Reverse complement sequence

CCATGGCAGCGAAATAATTAGTCGGTGACAGACAAGGCAGCTGGTGAAGAAGATGAAGATGCCTACTAGTGGCGACATAATAAGCCATCCGTGAAGGCGA[C/G]
GATACCAGTCGGTGGTGACGAAAGCAAGCCGACGGTGAAGATATAGACACGCATCAAAGACGATGACGAAGTCCACCAATCATGAAGATGAAGAAAATAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.90%	35.00%	1.35%	15.74%	NA
All Indica	2759	68.20%	8.40%	2.10%	21.24%	NA
All Japonica	1512	4.50%	84.90%	0.40%	10.19%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	77.00%	17.30%	0.84%	4.87%	NA
Indica II	465	88.40%	5.20%	1.29%	5.16%	NA
Indica III	913	58.80%	1.10%	2.19%	37.90%	NA
Indica Intermediate	786	60.60%	12.20%	3.44%	23.79%	NA
Temperate Japonica	767	0.50%	98.70%	0.00%	0.78%	NA
Tropical Japonica	504	7.70%	63.90%	1.19%	27.18%	NA
Japonica Intermediate	241	10.40%	85.10%	0.00%	4.56%	NA
VI/Aromatic	96	14.60%	84.40%	0.00%	1.04%	NA
Intermediate	90	38.90%	57.80%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818712613	G -> C	LOC_Os08g30420.1	downstream_gene_variant ; 4338.0bp to feature; MODIFIER	silent_mutation	Average:24.675; most accessible tissue: Zhenshan97 flower, score: 39.624	N	N	N	N
vg0818712613	G -> C	LOC_Os08g30410-LOC_Os08g30420	intergenic_region ; MODIFIER	silent_mutation	Average:24.675; most accessible tissue: Zhenshan97 flower, score: 39.624	N	N	N	N
vg0818712613	G -> DEL	N	N	silent_mutation	Average:24.675; most accessible tissue: Zhenshan97 flower, score: 39.624	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818712613	2.11E-06	2.11E-06	mr1499	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
vg0818712613	NA	2.57E-11	mr1553	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