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Detailed information for vg0122379413:

Variant ID: vg0122379413 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22379413
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, A: 0.36, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

CGACCAGGGGGACGCGCGCGCCTCGGACACGGTCGCCCCCTCGCCGCCCTCACCGTGTGAATCCCAGGAGCAACCCCACCATCTTGGCAAGGTTTTGAGT[A/C]
CTCATCCTCTCATCCACGTCCTTTTCCAAGCTCAAACCCCCCACCCTTTTTAATTTGTTCGTTCGTGCCCGCAGAGGCTGGAGGATGTGCTTATTTCCCT

Reverse complement sequence

AGGGAAATAAGCACATCCTCCAGCCTCTGCGGGCACGAACGAACAAATTAAAAAGGGTGGGGGGTTTGAGCTTGGAAAAGGACGTGGATGAGAGGATGAG[T/G]
ACTCAAAACCTTGCCAAGATGGTGGGGTTGCTCCTGGGATTCACACGGTGAGGGCGGCGAGGGGGCGACCGTGTCCGAGGCGCGCGCGTCCCCCTGGTCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.40%	36.00%	0.36%	10.26%	NA
All Indica	2759	75.20%	7.10%	0.62%	17.11%	NA
All Japonica	1512	5.10%	94.90%	0.00%	0.00%	NA
Aus	269	88.80%	9.70%	0.00%	1.49%	NA
Indica I	595	97.10%	0.30%	0.17%	2.35%	NA
Indica II	465	92.30%	2.20%	0.00%	5.59%	NA
Indica III	913	53.10%	13.80%	1.20%	31.87%	NA
Indica Intermediate	786	74.20%	7.30%	0.64%	17.94%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	13.30%	86.70%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	3.10%	0.00%	3.12%	NA
Intermediate	90	48.90%	44.40%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0122379413	A -> DEL	N	N	silent_mutation	Average:68.08; most accessible tissue: Zhenshan97 young leaf, score: 86.542	N	N	N	N
vg0122379413	A -> C	LOC_Os01g39670.1	downstream_gene_variant ; 1853.0bp to feature; MODIFIER	silent_mutation	Average:68.08; most accessible tissue: Zhenshan97 young leaf, score: 86.542	N	N	N	N
vg0122379413	A -> C	LOC_Os01g39680.1	intron_variant ; MODIFIER	silent_mutation	Average:68.08; most accessible tissue: Zhenshan97 young leaf, score: 86.542	N	N	N	N
vg0122379413	A -> C	LOC_Os01g39680.2	intron_variant ; MODIFIER	silent_mutation	Average:68.08; most accessible tissue: Zhenshan97 young leaf, score: 86.542	N	N	N	N
vg0122379413	A -> C	LOC_Os01g39680.3	intron_variant ; MODIFIER	silent_mutation	Average:68.08; most accessible tissue: Zhenshan97 young leaf, score: 86.542	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122379413	5.66E-06	5.33E-08	mr1380	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
vg0122379413	NA	9.02E-09	mr1439	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
vg0122379413	NA	6.59E-09	mr1561	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
vg0122379413	NA	4.37E-14	mr1653	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
vg0122379413	7.90E-06	7.90E-06	mr1875	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
vg0122379413	NA	1.75E-06	mr1908	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
vg0122379413	NA	3.54E-06	mr1561_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
vg0122379413	NA	9.53E-25	mr1653_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
vg0122379413	NA	7.42E-08	mr1681_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
vg0122379413	NA	6.78E-06	mr1908_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