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Detailed information for vg0809238968:

Variant ID: vg0809238968 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9238968
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTTGAGACTAATTGTGCGTTAGACCTACCCATATTCATACCTTTAAAACCAGATGAATGCGCATATCCTATCTTCCTATATAGTTATATAGTTAATACC[C/T]
ACTAAGAGGCATTTACTCCTATAAAGCAAAGCATGCAAGTAGCCACATCATCAATAATTCTAAGCCATCGGATCGTATTAGTACATAGTCATCAGCCGTT

Reverse complement sequence

AACGGCTGATGACTATGTACTAATACGATCCGATGGCTTAGAATTATTGATGATGTGGCTACTTGCATGCTTTGCTTTATAGGAGTAAATGCCTCTTAGT[G/A]
GGTATTAACTATATAACTATATAGGAAGATAGGATATGCGCATTCATCTGGTTTTAAAGGTATGAATATGGGTAGGTCTAACGCACAATTAGTCTCAAGC

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	97.00%	1.40%	1.59%	0.00%	NA
All Indica	2759	99.70%	0.00%	0.25%	0.00%	NA
All Japonica	1512	91.10%	4.40%	4.43%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.10%	0.00%	0.86%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	83.60%	8.70%	7.69%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg0809238968	C -> T	LOC_Os08g15230-LOC_Os08g15236	intergenic_region ; MODIFIER	silent_mutation	Average:55.088; most accessible tissue: Callus, score: 94.189	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809238968	NA	4.80E-06	mr1631_2	Jap_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
vg0809238968	2.65E-06	2.65E-06	mr1973_2	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