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Detailed information for vg0219846372:

Variant ID: vg0219846372 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19846372
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGTTGAAATGATTTGAAAAAAATGAATAGAGGATTGTAGCAAGGTTCTAGCCGCTCCGCAGCTCTACTCCAAACTATGGTCCTGAGTTAAATTTAGAAG[T/C]
TAGGGCCATACCAAATACTAGAAAAGACTACTTGTGAGGCATTAACAACCCTTGTTTGCTCTTCAACTTTTCTATGCATGTTTTAACGTTTTCTCCAAAA

Reverse complement sequence

TTTTGGAGAAAACGTTAAAACATGCATAGAAAAGTTGAAGAGCAAACAAGGGTTGTTAATGCCTCACAAGTAGTCTTTTCTAGTATTTGGTATGGCCCTA[A/G]
CTTCTAAATTTAACTCAGGACCATAGTTTGGAGTAGAGCTGCGGAGCGGCTAGAACCTTGCTACAATCCTCTATTCATTTTTTTCAAATCATTTCAACCC

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	90.50%	9.40%	0.11%	0.00%	NA
All Indica	2759	97.00%	3.00%	0.00%	0.00%	NA
All Japonica	1512	87.70%	12.00%	0.26%	0.00%	NA
Aus	269	62.10%	37.50%	0.37%	0.00%	NA
Indica I	595	91.40%	8.60%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	97.50%	2.50%	0.00%	0.00%	NA
Temperate Japonica	767	87.20%	12.40%	0.39%	0.00%	NA
Tropical Japonica	504	97.40%	2.60%	0.00%	0.00%	NA
Japonica Intermediate	241	68.90%	30.70%	0.41%	0.00%	NA
VI/Aromatic	96	27.10%	72.90%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0219846372	T -> C	LOC_Os02g33400.1	upstream_gene_variant ; 1204.0bp to feature; MODIFIER	silent_mutation	Average:52.485; most accessible tissue: Callus, score: 72.168	N	N	N	N
vg0219846372	T -> C	LOC_Os02g33410.1	downstream_gene_variant ; 1757.0bp to feature; MODIFIER	silent_mutation	Average:52.485; most accessible tissue: Callus, score: 72.168	N	N	N	N
vg0219846372	T -> C	LOC_Os02g33400-LOC_Os02g33410	intergenic_region ; MODIFIER	silent_mutation	Average:52.485; most accessible tissue: Callus, score: 72.168	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0219846372	2.51E-06	NA	mr1715	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
vg0219846372	NA	1.19E-06	mr1807	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
vg0219846372	NA	1.55E-08	mr1793_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