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Detailed information for vg0210599980:

Variant ID: vg0210599980 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10599980
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GGTATACCTTTCCCGTAGCCCTGACAGTAGCCCCCGACTTCTGCTTAAATGAACTCGTGAAACCGATTACGACTTCTGATGTCGAAGTTGTCGTCGTTCT[C/T,A]
AGTGTGATGACCGAGAGACAAGGAGTGATCGACAACGCCGGGTAAAGCTCAATGGTCATGAGTGAATTTAAATTTAAGTCCGAGAAACTGCCGCGCGTAA

Reverse complement sequence

TTACGCGCGGCAGTTTCTCGGACTTAAATTTAAATTCACTCATGACCATTGAGCTTTACCCGGCGTTGTCGATCACTCCTTGTCTCTCGGTCATCACACT[G/A,T]
AGAACGACGACAACTTCGACATCAGAAGTCGTAATCGGTTTCACGAGTTCATTTAAGCAGAAGTCGGGGGCTACTGTCAGGGCTACGGGAAAGGTATACC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.10%	9.50%	2.39%	7.05%	A: 0.02%
All Indica	2759	77.30%	8.00%	3.23%	11.49%	NA
All Japonica	1512	85.00%	13.50%	1.19%	0.26%	A: 0.07%
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	71.10%	11.80%	7.56%	9.58%	NA
Indica II	465	78.90%	3.00%	1.94%	16.13%	NA
Indica III	913	75.40%	10.10%	2.19%	12.38%	NA
Indica Intermediate	786	83.30%	5.60%	1.91%	9.16%	NA
Temperate Japonica	767	99.10%	0.10%	0.65%	0.13%	NA
Tropical Japonica	504	66.90%	30.60%	1.98%	0.60%	NA
Japonica Intermediate	241	78.00%	20.30%	1.24%	0.00%	A: 0.41%
VI/Aromatic	96	76.00%	13.50%	3.12%	7.29%	NA
Intermediate	90	81.10%	12.20%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210599980	C -> A	LOC_Os02g18270.1	upstream_gene_variant ; 3219.0bp to feature; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> A	LOC_Os02g18280.1	upstream_gene_variant ; 311.0bp to feature; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> A	LOC_Os02g18290.1	downstream_gene_variant ; 4197.0bp to feature; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> A	LOC_Os02g18270-LOC_Os02g18280	intergenic_region ; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> T	LOC_Os02g18270.1	upstream_gene_variant ; 3219.0bp to feature; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> T	LOC_Os02g18280.1	upstream_gene_variant ; 311.0bp to feature; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> T	LOC_Os02g18290.1	downstream_gene_variant ; 4197.0bp to feature; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> T	LOC_Os02g18270-LOC_Os02g18280	intergenic_region ; MODIFIER	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0210599980	C -> DEL	N	N	silent_mutation	Average:40.913; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210599980	8.00E-06	2.75E-07	mr1382	Jap_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
vg0210599980	NA	2.29E-06	mr1544	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
vg0210599980	2.41E-06	3.83E-09	mr1696	Jap_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