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Detailed information for vg0320863559:

Variant ID: vg0320863559 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20863559
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGGCTGTTTTTTAAATTTGCATGGTTATATACCTCTACACTTGTTCTTTATGGATAAGAACAGAGTATCTACACTTGTTCTTTTTTTACGCATAAGAA[T/C]
AGATTTTCTGCACTTGCTCTTTTCTTCTGGATTGATAAGAGAAGACTATCTAGACATGTTGTTTTAGTTAATTTGCCCCTGTTGTTGCTGCCCCTGTGGA

Reverse complement sequence

TCCACAGGGGCAGCAACAACAGGGGCAAATTAACTAAAACAACATGTCTAGATAGTCTTCTCTTATCAATCCAGAAGAAAAGAGCAAGTGCAGAAAATCT[A/G]
TTCTTATGCGTAAAAAAAGAACAAGTGTAGATACTCTGTTCTTATCCATAAAGAACAAGTGTAGAGGTATATAACCATGCAAATTTAAAAAACAGCCCAC

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	36.20%	0.10%	52.29%	11.38%	NA
All Indica	2759	8.10%	0.20%	74.05%	17.62%	NA
All Japonica	1512	87.60%	0.00%	10.19%	2.18%	NA
Aus	269	13.80%	0.00%	81.78%	4.46%	NA
Indica I	595	11.60%	0.30%	67.90%	20.17%	NA
Indica II	465	7.70%	0.00%	78.06%	14.19%	NA
Indica III	913	4.40%	0.00%	79.19%	16.43%	NA
Indica Intermediate	786	10.10%	0.50%	70.36%	19.08%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	67.10%	0.00%	27.18%	5.75%	NA
Japonica Intermediate	241	92.50%	0.00%	6.64%	0.83%	NA
VI/Aromatic	96	76.00%	0.00%	20.83%	3.12%	NA
Intermediate	90	57.80%	0.00%	37.78%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0320863559	T -> C	LOC_Os03g37620.1	upstream_gene_variant ; 967.0bp to feature; MODIFIER	silent_mutation	Average:24.267; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0320863559	T -> C	LOC_Os03g37630.1	upstream_gene_variant ; 529.0bp to feature; MODIFIER	silent_mutation	Average:24.267; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0320863559	T -> C	LOC_Os03g37610.1	downstream_gene_variant ; 1812.0bp to feature; MODIFIER	silent_mutation	Average:24.267; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0320863559	T -> C	LOC_Os03g37640.1	downstream_gene_variant ; 4766.0bp to feature; MODIFIER	silent_mutation	Average:24.267; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0320863559	T -> C	LOC_Os03g37640.2	downstream_gene_variant ; 4766.0bp to feature; MODIFIER	silent_mutation	Average:24.267; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0320863559	T -> C	LOC_Os03g37620-LOC_Os03g37630	intergenic_region ; MODIFIER	silent_mutation	Average:24.267; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0320863559	T -> DEL	N	N	silent_mutation	Average:24.267; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320863559	NA	3.38E-07	mr1136	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
vg0320863559	NA	1.48E-07	mr1217	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
vg0320863559	1.65E-06	9.52E-10	mr1718	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
vg0320863559	NA	3.50E-06	mr1750	Ind_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
vg0320863559	NA	2.41E-06	mr1830	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
vg0320863559	NA	4.09E-07	mr1845	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
vg0320863559	NA	7.10E-08	mr1852	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
vg0320863559	NA	1.76E-08	mr1136_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
vg0320863559	6.30E-06	2.41E-14	mr1750_2	Ind_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