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Detailed information for vg0208038424:

Variant ID: vg0208038424 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8038424
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCTTTCATATTTTAATGTATGACGCTGTTGACTTTTTAACCAGCGTTTGACCATTCATTTTATTCAAATTTTTTGTGCAAATATGAAAATATTTATAT[C/T]
ATGCTTAAAGAACATTTGATGATGAATCAAGTCACAATAAAATAAATGATAATTACATAAATTTTTTAAATAATACGAATGATCAAACGTTGGATAAAAA

Reverse complement sequence

TTTTTATCCAACGTTTGATCATTCGTATTATTTAAAAAATTTATGTAATTATCATTTATTTTATTGTGACTTGATTCATCATCAAATGTTCTTTAAGCAT[G/A]
ATATAAATATTTTCATATTTGCACAAAAAATTTGAATAAAATGAATGGTCAAACGCTGGTTAAAAAGTCAACAGCGTCATACATTAAAATATGAAAGAAG

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	51.30%	0.10%	0.23%	48.35%	NA
All Indica	2759	30.30%	0.20%	0.40%	69.08%	NA
All Japonica	1512	98.10%	0.00%	0.00%	1.92%	NA
Aus	269	5.20%	0.00%	0.00%	94.80%	NA
Indica I	595	36.30%	0.00%	0.50%	63.19%	NA
Indica II	465	17.60%	0.40%	0.00%	81.94%	NA
Indica III	913	34.60%	0.00%	0.22%	65.17%	NA
Indica Intermediate	786	28.40%	0.40%	0.76%	70.48%	NA
Temperate Japonica	767	98.60%	0.00%	0.00%	1.43%	NA
Tropical Japonica	504	97.80%	0.00%	0.00%	2.18%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	44.80%	0.00%	0.00%	55.21%	NA
Intermediate	90	53.30%	0.00%	0.00%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208038424	C -> T	LOC_Os02g14570.1	upstream_gene_variant ; 2967.0bp to feature; MODIFIER	silent_mutation	Average:39.078; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N
vg0208038424	C -> T	LOC_Os02g14580.1	upstream_gene_variant ; 2689.0bp to feature; MODIFIER	silent_mutation	Average:39.078; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N
vg0208038424	C -> T	LOC_Os02g14570-LOC_Os02g14580	intergenic_region ; MODIFIER	silent_mutation	Average:39.078; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N
vg0208038424	C -> DEL	N	N	silent_mutation	Average:39.078; most accessible tissue: Zhenshan97 root, score: 86.252	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208038424	2.07E-06	2.07E-06	mr1770	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