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Detailed information for vg0208695804:

Variant ID: vg0208695804 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8695804
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGCATTGTCAGCCATACAAAATACGAAGCAAAGCGAACGGCACATCAAACACAAATACATATAATCTCTAAAACAGATCAGGATACATAGATAAGATTA[G/C]
AAATGACATGAGTGGATGCAAATACTGTTCAGGCGATGAATTGAAGATCTGGTGATCAAGGCACATGTATAACTTTGATTGCAGTAGTAGTGTCACGCAT

Reverse complement sequence

ATGCGTGACACTACTACTGCAATCAAAGTTATACATGTGCCTTGATCACCAGATCTTCAATTCATCGCCTGAACAGTATTTGCATCCACTCATGTCATTT[C/G]
TAATCTTATCTATGTATCCTGATCTGTTTTAGAGATTATATGTATTTGTGTTTGATGTGCCGTTCGCTTTGCTTCGTATTTTGTATGGCTGACAATGCTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.60%	3.50%	0.89%	0.00%	NA
All Indica	2759	99.30%	0.00%	0.72%	0.00%	NA
All Japonica	1512	87.70%	11.00%	1.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	0.00%	1.51%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.00%	1.02%	0.00%	NA
Temperate Japonica	767	77.80%	19.80%	2.35%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	94.20%	5.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	3.33%	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
vg0208695804	G -> C	LOC_Os02g15520.1	downstream_gene_variant ; 4621.0bp to feature; MODIFIER	silent_mutation	Average:22.195; most accessible tissue: Callus, score: 39.527	N	N	N	N
vg0208695804	G -> C	LOC_Os02g15520.2	downstream_gene_variant ; 4621.0bp to feature; MODIFIER	silent_mutation	Average:22.195; most accessible tissue: Callus, score: 39.527	N	N	N	N
vg0208695804	G -> C	LOC_Os02g15510.1	intron_variant ; MODIFIER	silent_mutation	Average:22.195; most accessible tissue: Callus, score: 39.527	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208695804	NA	3.17E-08	mr1045	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
vg0208695804	NA	8.48E-07	mr1045	Jap_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
vg0208695804	7.28E-06	NA	mr1203	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
vg0208695804	NA	8.86E-06	mr1210	Jap_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
vg0208695804	6.31E-06	NA	mr1585	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
vg0208695804	NA	1.09E-08	mr1585	Jap_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
vg0208695804	NA	5.33E-06	mr1586	Jap_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
vg0208695804	6.91E-06	NA	mr1897	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
vg0208695804	2.68E-06	1.45E-06	mr1897	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
vg0208695804	4.02E-06	NA	mr1071_2	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
vg0208695804	2.64E-06	NA	mr1203_2	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
vg0208695804	4.93E-06	NA	mr1305_2	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
vg0208695804	NA	1.20E-07	mr1305_2	Jap_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
vg0208695804	1.08E-06	NA	mr1317_2	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
vg0208695804	5.94E-06	5.95E-06	mr1317_2	Jap_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
vg0208695804	2.72E-08	7.76E-09	mr1585_2	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
vg0208695804	9.53E-06	5.80E-11	mr1585_2	Jap_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
vg0208695804	7.70E-06	NA	mr1619_2	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
vg0208695804	2.01E-07	NA	mr1897_2	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
vg0208695804	2.21E-06	2.21E-06	mr1897_2	Jap_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