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Detailed information for vg0221622425:

Variant ID: vg0221622425 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21622425
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATTGACTGTAACTCTCTAAGCAAAAGCCATGATTATATTTCATTATATAAAAAAAAAACTGGCGTATCTCTTTACATGCATGATGAGACTTCTAAGCG[C/T]
CGTCCCTCTCGTCGTTTTCTTGACCGGATGAATCTCCTCTCTTGACTTTGACCTGTCAAGAGGTTAGTTGACTTGAAATCAAATACAATATGTTTCTCTA

Reverse complement sequence

TAGAGAAACATATTGTATTTGATTTCAAGTCAACTAACCTCTTGACAGGTCAAAGTCAAGAGAGGAGATTCATCCGGTCAAGAAAACGACGAGAGGGACG[G/A]
CGCTTAGAAGTCTCATCATGCATGTAAAGAGATACGCCAGTTTTTTTTTTATATAATGAAATATAATCATGGCTTTTGCTTAGAGAGTTACAGTCAATTA

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	93.30%	4.00%	2.62%	0.00%	NA
All Indica	2759	89.20%	6.40%	4.35%	0.00%	NA
All Japonica	1512	99.30%	0.40%	0.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	76.10%	10.80%	13.11%	0.00%	NA
Indica II	465	84.90%	12.90%	2.15%	0.00%	NA
Indica III	913	99.60%	0.00%	0.44%	0.00%	NA
Indica Intermediate	786	89.70%	6.70%	3.56%	0.00%	NA
Temperate Japonica	767	99.10%	0.70%	0.26%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0221622425	C -> T	LOC_Os02g36000.1	upstream_gene_variant ; 2597.0bp to feature; MODIFIER	silent_mutation	Average:58.163; most accessible tissue: Callus, score: 92.859	N	N	N	N
vg0221622425	C -> T	LOC_Os02g35980.1	downstream_gene_variant ; 3654.0bp to feature; MODIFIER	silent_mutation	Average:58.163; most accessible tissue: Callus, score: 92.859	N	N	N	N
vg0221622425	C -> T	LOC_Os02g35980-LOC_Os02g36000	intergenic_region ; MODIFIER	silent_mutation	Average:58.163; most accessible tissue: Callus, score: 92.859	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221622425	NA	1.15E-06	mr1038	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
vg0221622425	NA	1.57E-07	mr1038	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
vg0221622425	NA	1.25E-08	mr1389	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
vg0221622425	NA	1.01E-08	mr1389	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
vg0221622425	NA	4.19E-07	mr1038_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
vg0221622425	NA	1.04E-07	mr1038_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
vg0221622425	NA	7.34E-06	mr1389_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
vg0221622425	NA	8.23E-07	mr1389_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
vg0221622425	3.82E-07	3.82E-07	mr1416_2	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