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Detailed information for vg0715470958:

Variant ID: vg0715470958 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15470958
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGTTCCAGGAGGCAAATAGTATCCTCTATTAACCTTGTTTGAAGACGATGAAGCCCTCACATCGCCCTTTGCAGCCCTCTCATCAAACCGACGCTGGAG[C/T]
CCGGTCTGACCGGCTGCAGACCACCGGTCAGACCGGCCAGACGCGTCGGTCAGACCGACGTGTGGCGCACGGTCGGACCGGCCTGAGGCATCGGTCAGAC

Reverse complement sequence

GTCTGACCGATGCCTCAGGCCGGTCCGACCGTGCGCCACACGTCGGTCTGACCGACGCGTCTGGCCGGTCTGACCGGTGGTCTGCAGCCGGTCAGACCGG[G/A]
CTCCAGCGTCGGTTTGATGAGAGGGCTGCAAAGGGCGATGTGAGGGCTTCATCGTCTTCAAACAAGGTTAATAGAGGATACTATTTGCCTCCTGGAACAG

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	47.90%	0.20%	7.28%	44.63%	NA
All Indica	2759	47.10%	0.10%	8.23%	44.51%	NA
All Japonica	1512	46.20%	0.10%	6.48%	47.22%	NA
Aus	269	54.60%	0.40%	1.49%	43.49%	NA
Indica I	595	29.10%	0.00%	4.20%	66.72%	NA
Indica II	465	40.60%	0.00%	12.04%	47.31%	NA
Indica III	913	61.30%	0.30%	9.86%	28.48%	NA
Indica Intermediate	786	48.10%	0.10%	7.12%	44.66%	NA
Temperate Japonica	767	75.00%	0.00%	1.96%	23.08%	NA
Tropical Japonica	504	10.90%	0.20%	11.51%	77.38%	NA
Japonica Intermediate	241	28.60%	0.00%	10.37%	61.00%	NA
VI/Aromatic	96	67.70%	2.10%	11.46%	18.75%	NA
Intermediate	90	60.00%	0.00%	4.44%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715470958	C -> DEL	LOC_Os07g26780.1	N	frameshift_variant	Average:15.195; most accessible tissue: Callus, score: 27.373	N	N	N	N
vg0715470958	C -> T	LOC_Os07g26780.1	synonymous_variant ; p.Gly836Gly; LOW	synonymous_codon	Average:15.195; most accessible tissue: Callus, score: 27.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715470958	4.76E-06	4.76E-06	mr1313	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
vg0715470958	NA	8.54E-06	mr1497_2	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