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Detailed information for vg0312620511:

Variant ID: vg0312620511 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 12620511
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCTCTTATCCACATAAACAAAAGATCTCTCTCTCCCTTATCCACACTCACAGAAACAAGAGGGGAGGCTCTTGCGGGGTGGCGGAGGACCCGACGGCC[C/A]
CCGAGAGAGGCGGCGGCGCTAGGCGGCGAGCGGCGGTGGCGGTACCCACATCCTCCTCCCCCTTCTTTCTCCCCTCCTCCCCCTTCTCTTATTTCCGATC

Reverse complement sequence

GATCGGAAATAAGAGAAGGGGGAGGAGGGGAGAAAGAAGGGGGAGGAGGATGTGGGTACCGCCACCGCCGCTCGCCGCCTAGCGCCGCCGCCTCTCTCGG[G/T]
GGCCGTCGGGTCCTCCGCCACCCCGCAAGAGCCTCCCCTCTTGTTTCTGTGAGTGTGGATAAGGGAGAGAGAGATCTTTTGTTTATGTGGATAAGAGAGT

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	68.60%	17.90%	11.57%	1.95%	NA
All Indica	2759	48.70%	29.20%	18.85%	3.23%	NA
All Japonica	1512	98.40%	0.90%	0.73%	0.00%	NA
Aus	269	94.80%	2.20%	2.97%	0.00%	NA
Indica I	595	68.60%	10.80%	19.33%	1.34%	NA
Indica II	465	29.50%	33.80%	24.30%	12.47%	NA
Indica III	913	47.20%	37.80%	14.79%	0.22%	NA
Indica Intermediate	786	46.70%	30.70%	19.97%	2.67%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	97.40%	1.60%	0.99%	0.00%	NA
Japonica Intermediate	241	97.10%	1.20%	1.66%	0.00%	NA
VI/Aromatic	96	94.80%	2.10%	1.04%	2.08%	NA
Intermediate	90	73.30%	17.80%	7.78%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0312620511	C -> A	LOC_Os03g22020.1	upstream_gene_variant ; 893.0bp to feature; MODIFIER	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0312620511	C -> A	LOC_Os03g22010.1	downstream_gene_variant ; 3345.0bp to feature; MODIFIER	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0312620511	C -> A	LOC_Os03g22030.1	downstream_gene_variant ; 3373.0bp to feature; MODIFIER	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0312620511	C -> A	LOC_Os03g22010.4	downstream_gene_variant ; 3345.0bp to feature; MODIFIER	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0312620511	C -> A	LOC_Os03g22010.3	downstream_gene_variant ; 3345.0bp to feature; MODIFIER	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0312620511	C -> A	LOC_Os03g22010.2	downstream_gene_variant ; 3345.0bp to feature; MODIFIER	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0312620511	C -> A	LOC_Os03g22020-LOC_Os03g22030	intergenic_region ; MODIFIER	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg0312620511	C -> DEL	N	N	silent_mutation	Average:55.213; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0312620511	NA	7.48E-06	mr1542	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
vg0312620511	3.92E-06	NA	mr1935	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
vg0312620511	NA	4.12E-06	mr1542_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