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Detailed information for vg1015834424:

Variant ID: vg1015834424 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 15834424
Reference Allele: C	Alternative Allele: G,T
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GCAATCCAGGCATTTAGAAAAATATCTCACCTCTTTTGACATGGAAATAATAAAATAATACAATCGGTGTCCTACTACCAATTATACGTATGTTTAGTAT[C/G,T]
CATCAGCCCTATCACGTTTACATGGTGTCTCCCAACAAATTACATGTTTTTTACGTGTCCTGTGGCAAATTTTGCCATCTAAAAATGCCGAATCATATGA

Reverse complement sequence

TCATATGATTCGGCATTTTTAGATGGCAAAATTTGCCACAGGACACGTAAAAAACATGTAATTTGTTGGGAGACACCATGTAAACGTGATAGGGCTGATG[G/C,A]
ATACTAAACATACGTATAATTGGTAGTAGGACACCGATTGTATTATTTTATTATTTCCATGTCAAAAGAGGTGAGATATTTTTCTAAATGCCTGGATTGC

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	89.30%	10.70%	0.02%	0.00%	T: 0.02%
All Indica	2759	99.50%	0.50%	0.04%	0.00%	NA
All Japonica	1512	70.10%	29.80%	0.00%	0.00%	T: 0.07%
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.10%	0.13%	0.00%	NA
Temperate Japonica	767	97.50%	2.50%	0.00%	0.00%	NA
Tropical Japonica	504	23.00%	77.00%	0.00%	0.00%	NA
Japonica Intermediate	241	81.30%	18.30%	0.00%	0.00%	T: 0.41%
VI/Aromatic	96	74.00%	26.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg1015834424	C -> G	LOC_Os10g30460.1	upstream_gene_variant ; 2580.0bp to feature; MODIFIER	silent_mutation	Average:58.666; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg1015834424	C -> G	LOC_Os10g30460-LOC_Os10g30480	intergenic_region ; MODIFIER	silent_mutation	Average:58.666; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg1015834424	C -> T	LOC_Os10g30460.1	upstream_gene_variant ; 2580.0bp to feature; MODIFIER	silent_mutation	Average:58.666; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg1015834424	C -> T	LOC_Os10g30460-LOC_Os10g30480	intergenic_region ; MODIFIER	silent_mutation	Average:58.666; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1015834424	NA	6.61E-08	mr1248	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
vg1015834424	NA	7.89E-11	mr1248	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
vg1015834424	NA	4.37E-07	mr1338	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
vg1015834424	NA	3.99E-07	mr1425	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
vg1015834424	NA	9.10E-06	mr1425	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
vg1015834424	NA	8.87E-07	mr1527	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
vg1015834424	1.63E-06	NA	mr1530	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
vg1015834424	1.16E-06	1.21E-08	mr1530	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
vg1015834424	NA	9.39E-12	mr1540	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
vg1015834424	NA	2.30E-10	mr1623	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
vg1015834424	NA	9.85E-08	mr1642	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
vg1015834424	NA	3.94E-06	mr1642	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
vg1015834424	NA	2.68E-31	mr1699	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
vg1015834424	NA	8.37E-14	mr1732	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
vg1015834424	NA	1.34E-07	mr1653_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
vg1015834424	NA	4.92E-08	mr1696_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
vg1015834424	NA	2.30E-30	mr1699_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
vg1015834424	NA	9.84E-10	mr1705_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
vg1015834424	NA	4.24E-07	mr1819_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
vg1015834424	NA	1.69E-10	mr1905_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