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Detailed information for vg0221202752:

Variant ID: vg0221202752 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21202752
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACTGATCCCCATCCATTCCCAGCCATTTCCAAAGCAAATCGCATCATCCAATTCACATTCATGGCAGAGGAGAGAGAAAGCTTCAAGAGCCAATGGGCG[C/T]
CCTCCGACGTCACCGAGGAGAGCTTGAAGGAAATGGTAGTACATGGTGTTCTTTCGGCAAAGGAGATCATTGGATGGCGTCCGGCGTACGGCGAAGCATT

Reverse complement sequence

AATGCTTCGCCGTACGCCGGACGCCATCCAATGATCTCCTTTGCCGAAAGAACACCATGTACTACCATTTCCTTCAAGCTCTCCTCGGTGACGTCGGAGG[G/A]
CGCCCATTGGCTCTTGAAGCTTTCTCTCTCCTCTGCCATGAATGTGAATTGGATGATGCGATTTGCTTTGGAAATGGCTGGGAATGGATGGGGATCAGTG

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	94.40%	3.80%	1.78%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	83.10%	11.50%	5.36%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	76.10%	16.40%	7.43%	0.00%	NA
Tropical Japonica	504	97.60%	1.40%	0.99%	0.00%	NA
Japonica Intermediate	241	75.10%	17.00%	7.88%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	2.22%	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
vg0221202752	C -> T	LOC_Os02g35280.1	upstream_gene_variant ; 575.0bp to feature; MODIFIER	silent_mutation	Average:49.237; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg0221202752	C -> T	LOC_Os02g35290.1	downstream_gene_variant ; 3686.0bp to feature; MODIFIER	silent_mutation	Average:49.237; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg0221202752	C -> T	LOC_Os02g35270-LOC_Os02g35280	intergenic_region ; MODIFIER	silent_mutation	Average:49.237; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221202752	4.02E-06	1.28E-08	mr1691_2	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
vg0221202752	9.47E-06	NA	mr1720_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