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Detailed information for vg0107004493:

Variant ID: vg0107004493 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 7004493
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTGATATATAGATCAGAGATAGTATATACTCGCTCCCTCCCGAAAAAAAACTAATCTAGGATGGGATTTAACCTCTCCTAGTTATCTAGATTAATTGTA[C/T]
TAAGAGGAGTCATATCTTCTTCTAGGTTGGGTTTTTTTTGGGACCGAGAGAGTATGTACTAGAAAAATAGGAGTATATGATTTTATAAATGCAGGGTATA

Reverse complement sequence

TATACCCTGCATTTATAAAATCATATACTCCTATTTTTCTAGTACATACTCTCTCGGTCCCAAAAAAAACCCAACCTAGAAGAAGATATGACTCCTCTTA[G/A]
TACAATTAATCTAGATAACTAGGAGAGGTTAAATCCCATCCTAGATTAGTTTTTTTTCGGGAGGGAGCGAGTATATACTATCTCTGATCTATATATCAAG

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	98.20%	0.70%	1.02%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.14%	0.00%	NA
All Japonica	1512	94.80%	2.30%	2.91%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	90.00%	4.60%	5.48%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0107004493	C -> T	LOC_Os01g12690.1	upstream_gene_variant ; 4540.0bp to feature; MODIFIER	silent_mutation	Average:58.804; most accessible tissue: Callus, score: 93.292	N	N	N	N
vg0107004493	C -> T	LOC_Os01g12680-LOC_Os01g12690	intergenic_region ; MODIFIER	silent_mutation	Average:58.804; most accessible tissue: Callus, score: 93.292	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0107004493	1.31E-06	1.30E-06	mr1527	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