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Detailed information for vg0715481030:

Variant ID: vg0715481030 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15481030
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 34. )

Flanking Sequence (100 bp) in Reference Genome:

CACTGTCTCCCAGCTTTCGTTCCAGCGCTTTCCGCTACATTGTTCTCACTAGTGGAGAAACCATTTTTGCTCGGTCGACCAAAAACCACAATAGTCCCGG[T/C]
TGCAGTAAAAACCGGGACTAAAGATGGTTTTTAGTCCCGGTTTATAAGCAGAACGGGACAACGTGTTCTTTAGTCCCGGTTGGTGTTACCCGGTTCACAT

Reverse complement sequence

ATGTGAACCGGGTAACACCAACCGGGACTAAAGAACACGTTGTCCCGTTCTGCTTATAAACCGGGACTAAAAACCATCTTTAGTCCCGGTTTTTACTGCA[A/G]
CCGGGACTATTGTGGTTTTTGGTCGACCGAGCAAAAATGGTTTCTCCACTAGTGAGAACAATGTAGCGGAAAGCGCTGGAACGAAAGCTGGGAGACAGTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.70%	4.50%	16.38%	16.44%	NA
All Indica	2759	61.80%	5.30%	18.88%	14.03%	NA
All Japonica	1512	66.00%	0.00%	11.04%	22.95%	NA
Aus	269	43.90%	23.80%	25.65%	6.69%	NA
Indica I	595	70.30%	0.50%	20.50%	8.74%	NA
Indica II	465	38.70%	10.10%	29.68%	21.51%	NA
Indica III	913	68.90%	4.70%	11.28%	15.12%	NA
Indica Intermediate	786	60.80%	6.70%	20.10%	12.34%	NA
Temperate Japonica	767	80.80%	0.00%	5.61%	13.56%	NA
Tropical Japonica	504	47.80%	0.00%	15.28%	36.90%	NA
Japonica Intermediate	241	56.80%	0.00%	19.50%	23.65%	NA
VI/Aromatic	96	85.40%	1.00%	3.12%	10.42%	NA
Intermediate	90	65.60%	2.20%	15.56%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715481030	T -> DEL	N	N	silent_mutation	Average:15.367; most accessible tissue: Callus, score: 44.317	N	N	N	N
vg0715481030	T -> C	LOC_Os07g26790.1	downstream_gene_variant ; 4846.0bp to feature; MODIFIER	silent_mutation	Average:15.367; most accessible tissue: Callus, score: 44.317	N	N	N	N
vg0715481030	T -> C	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
vg0715481030	NA	6.33E-07	mr1062	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
vg0715481030	3.72E-06	6.24E-13	mr1062_2	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