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Detailed information for vg0714136537:

Variant ID: vg0714136537 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14136537
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGCTATTTTGAAGAAAAATTTGAAGATGTGGGAAGAATGTTTGCCTCATATGGAGTTTGCATACAATCGGGCAACACATTCTACTACCAAGGTAAGTT[C/T]
TTTTCAGGTAGTGTATGGTTTCAACCCTCGTGCTCCAATTGATATGTTGCCTTTACCTACTAGTGAGAGGGTTCATAATGATGCTAAGGCACGCGCTGAA

Reverse complement sequence

TTCAGCGCGTGCCTTAGCATCATTATGAACCCTCTCACTAGTAGGTAAAGGCAACATATCAATTGGAGCACGAGGGTTGAAACCATACACTACCTGAAAA[G/A]
AACTTACCTTGGTAGTAGAATGTGTTGCCCGATTGTATGCAAACTCCATATGAGGCAAACATTCTTCCCACATCTTCAAATTTTTCTTCAAAATAGCCCT

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	37.50%	1.10%	31.06%	30.34%	NA
All Indica	2759	33.50%	1.30%	41.61%	23.63%	NA
All Japonica	1512	50.80%	0.30%	2.18%	46.69%	NA
Aus	269	15.20%	1.10%	68.77%	14.87%	NA
Indica I	595	49.70%	0.70%	9.41%	40.17%	NA
Indica II	465	37.00%	0.60%	39.57%	22.80%	NA
Indica III	913	17.90%	2.10%	66.70%	13.36%	NA
Indica Intermediate	786	37.30%	1.10%	38.04%	23.54%	NA
Temperate Japonica	767	73.10%	0.00%	1.69%	25.16%	NA
Tropical Japonica	504	20.00%	1.00%	1.79%	77.18%	NA
Japonica Intermediate	241	44.00%	0.00%	4.56%	51.45%	NA
VI/Aromatic	96	3.10%	8.30%	75.00%	13.54%	NA
Intermediate	90	38.90%	2.20%	33.33%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714136537	C -> DEL	N	N	silent_mutation	Average:12.167; most accessible tissue: Callus, score: 32.367	N	N	N	N
vg0714136537	C -> T	LOC_Os07g24850.1	downstream_gene_variant ; 3539.0bp to feature; MODIFIER	silent_mutation	Average:12.167; most accessible tissue: Callus, score: 32.367	N	N	N	N
vg0714136537	C -> T	LOC_Os07g24850-LOC_Os07g24870	intergenic_region ; MODIFIER	silent_mutation	Average:12.167; most accessible tissue: Callus, score: 32.367	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714136537	9.01E-07	8.98E-07	mr1703	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
vg0714136537	1.93E-06	1.92E-06	mr1703	Jap_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