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Detailed information for vg0223147995:

Variant ID: vg0223147995 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23147995
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTTCAACTTGCTTTTTCATTTGTTCCATTCTGGCGGCTTGCGCTGTTTGAGATCCAGATGGTTGAGGATACAGTTATGTTGGCCTAAATCAATGGAAC[A/G]
GATCTGGATGATTACCTTTTGATGAACCACTTAGTTCGAAGTTTGCATCCTGGAGCTGAGCGATTCGATCCCTTAACTCCTTCTCCGTCTTCTTGGCGTG

Reverse complement sequence

CACGCCAAGAAGACGGAGAAGGAGTTAAGGGATCGAATCGCTCAGCTCCAGGATGCAAACTTCGAACTAAGTGGTTCATCAAAAGGTAATCATCCAGATC[T/C]
GTTCCATTGATTTAGGCCAACATAACTGTATCCTCAACCATCTGGATCTCAAACAGCGCAAGCCGCCAGAATGGAACAAATGAAAAAGCAAGTTGAAGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.60%	0.10%	1.46%	73.85%	NA
All Indica	2759	3.40%	0.20%	1.12%	95.25%	NA
All Japonica	1512	66.70%	0.10%	1.85%	31.35%	NA
Aus	269	1.10%	0.00%	0.37%	98.51%	NA
Indica I	595	4.70%	0.70%	2.02%	92.61%	NA
Indica II	465	1.90%	0.00%	0.65%	97.42%	NA
Indica III	913	1.80%	0.10%	1.20%	96.93%	NA
Indica Intermediate	786	5.30%	0.00%	0.64%	94.02%	NA
Temperate Japonica	767	82.40%	0.00%	1.96%	15.65%	NA
Tropical Japonica	504	36.50%	0.20%	1.98%	61.31%	NA
Japonica Intermediate	241	80.10%	0.00%	1.24%	18.67%	NA
VI/Aromatic	96	28.10%	0.00%	7.29%	64.58%	NA
Intermediate	90	30.00%	0.00%	2.22%	67.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223147995	A -> G	LOC_Os02g38260.1	downstream_gene_variant ; 3723.0bp to feature; MODIFIER	silent_mutation	Average:11.246; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0223147995	A -> G	LOC_Os02g38270.1	downstream_gene_variant ; 998.0bp to feature; MODIFIER	silent_mutation	Average:11.246; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0223147995	A -> G	LOC_Os02g38290.1	downstream_gene_variant ; 4697.0bp to feature; MODIFIER	silent_mutation	Average:11.246; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0223147995	A -> G	LOC_Os02g38290.2	downstream_gene_variant ; 4694.0bp to feature; MODIFIER	silent_mutation	Average:11.246; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0223147995	A -> G	LOC_Os02g38280.1	intron_variant ; MODIFIER	silent_mutation	Average:11.246; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0223147995	A -> DEL	N	N	silent_mutation	Average:11.246; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223147995	NA	3.32E-06	mr1083	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
vg0223147995	NA	6.47E-08	mr1226	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
vg0223147995	NA	4.19E-08	mr1411	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
vg0223147995	1.36E-06	NA	mr1298_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
vg0223147995	3.52E-06	NA	mr1731_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
vg0223147995	NA	7.26E-06	mr1736_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
vg0223147995	9.42E-06	NA	mr1743_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
vg0223147995	2.00E-06	NA	mr1944_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