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Detailed information for vg0715481027:

Variant ID: vg0715481027 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15481027
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCCACTGTCTCCCAGCTTTCGTTCCAGCGCTTTCCGCTACATTGTTCTCACTAGTGGAGAAACCATTTTTGCTCGGTCGACCAAAAACCACAATAGTCC[C/T]
GGTTGCAGTAAAAACCGGGACTAAAGATGGTTTTTAGTCCCGGTTTATAAGCAGAACGGGACAACGTGTTCTTTAGTCCCGGTTGGTGTTACCCGGTTCA

Reverse complement sequence

TGAACCGGGTAACACCAACCGGGACTAAAGAACACGTTGTCCCGTTCTGCTTATAAACCGGGACTAAAAACCATCTTTAGTCCCGGTTTTTACTGCAACC[G/A]
GGACTATTGTGGTTTTTGGTCGACCGAGCAAAAATGGTTTCTCCACTAGTGAGAACAATGTAGCGGAAAGCGCTGGAACGAAAGCTGGGAGACAGTGGCG

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	67.00%	6.90%	18.51%	7.53%	NA
All Indica	2759	64.90%	11.70%	20.15%	3.26%	NA
All Japonica	1512	64.70%	0.20%	18.25%	16.87%	NA
Aus	269	93.30%	0.00%	6.69%	0.00%	NA
Indica I	595	88.90%	1.20%	8.91%	1.01%	NA
Indica II	465	60.60%	6.20%	26.88%	6.24%	NA
Indica III	913	50.20%	23.80%	22.34%	3.72%	NA
Indica Intermediate	786	66.40%	8.80%	22.14%	2.67%	NA
Temperate Japonica	767	80.20%	0.00%	9.65%	10.17%	NA
Tropical Japonica	504	46.60%	0.40%	25.99%	26.98%	NA
Japonica Intermediate	241	53.10%	0.40%	29.46%	17.01%	NA
VI/Aromatic	96	86.50%	0.00%	6.25%	7.29%	NA
Intermediate	90	72.20%	2.20%	21.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715481027	C -> DEL	N	N	silent_mutation	Average:15.367; most accessible tissue: Callus, score: 44.317	N	N	N	N
vg0715481027	C -> T	LOC_Os07g26790.1	downstream_gene_variant ; 4849.0bp to feature; MODIFIER	silent_mutation	Average:15.367; most accessible tissue: Callus, score: 44.317	N	N	N	N
vg0715481027	C -> T	LOC_Os07g26780-LOC_Os07g26790	intergenic_region ; MODIFIER	silent_mutation	Average:15.367; most accessible tissue: Callus, score: 44.317	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715481027	NA	7.76E-06	mr1305	Ind_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
vg0715481027	1.48E-06	5.90E-06	mr1972	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