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Detailed information for vg0210290709:

Variant ID: vg0210290709 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10290709
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATACCCTCCAACCGCCATAGGGGAGCAATCCACACCGCCCATCCAAACCCTGCATCCAGCGGCTTCACGGCAGGTTCGGCCGAACCCCCAGGTTCAGC[C/T]
GAACCAGGGGCCGGCCCAACCAGCCCACATTTTGGCTGGTGGTCTCGTCCGCTGCTTCACTTCATAGACTTATGAATTTTGGCCCAATTCATCGTGTCAA

Reverse complement sequence

TTGACACGATGAATTGGGCCAAAATTCATAAGTCTATGAAGTGAAGCAGCGGACGAGACCACCAGCCAAAATGTGGGCTGGTTGGGCCGGCCCCTGGTTC[G/A]
GCTGAACCTGGGGGTTCGGCCGAACCTGCCGTGAAGCCGCTGGATGCAGGGTTTGGATGGGCGGTGTGGATTGCTCCCCTATGGCGGTTGGAGGGTATTA

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	85.20%	3.20%	7.09%	4.53%	NA
All Indica	2759	75.90%	5.20%	11.45%	7.43%	NA
All Japonica	1512	98.80%	0.00%	0.66%	0.53%	NA
Aus	269	97.80%	1.10%	1.12%	0.00%	NA
Indica I	595	82.70%	1.80%	11.60%	3.87%	NA
Indica II	465	72.50%	5.80%	15.27%	6.45%	NA
Indica III	913	71.20%	7.20%	10.19%	11.39%	NA
Indica Intermediate	786	78.20%	5.10%	10.56%	6.11%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	96.60%	0.00%	1.79%	1.59%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	2.20%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210290709	C -> T	LOC_Os02g17790.1	downstream_gene_variant ; 1799.0bp to feature; MODIFIER	silent_mutation	Average:50.327; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg0210290709	C -> T	LOC_Os02g17780-LOC_Os02g17790	intergenic_region ; MODIFIER	silent_mutation	Average:50.327; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg0210290709	C -> DEL	N	N	silent_mutation	Average:50.327; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210290709	3.07E-06	3.07E-06	mr1025	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
vg0210290709	3.85E-06	3.85E-06	mr1501	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