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Detailed information for vg0712960415:

Variant ID: vg0712960415 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12960415
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACACACCTCAAGCAATAGCTCTCTCATTTCTCTCAAGTTTAGTTTAGTAGTATCTAGCTGGTGGAATAGGAATAGAGTAGAAATCAGGAGTTCGGAAG[T/C]
CTTCGGAAGAGTTCGGGTATGGCTCTAGTAGCTTTTTTCTTCTCTTTTGTAAGCTTTGTACTTTTATTAGAATACTCTTCTAAATACATTTATGGTATTG

Reverse complement sequence

CAATACCATAAATGTATTTAGAAGAGTATTCTAATAAAAGTACAAAGCTTACAAAAGAGAAGAAAAAAGCTACTAGAGCCATACCCGAACTCTTCCGAAG[A/G]
CTTCCGAACTCCTGATTTCTACTCTATTCCTATTCCACCAGCTAGATACTACTAAACTAAACTTGAGAGAAATGAGAGAGCTATTGCTTGAGGTGTGTGT

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	73.20%	1.60%	10.79%	14.43%	NA
All Indica	2759	64.20%	1.80%	16.13%	17.87%	NA
All Japonica	1512	89.70%	1.10%	1.79%	7.34%	NA
Aus	269	62.10%	1.90%	11.15%	24.91%	NA
Indica I	595	57.60%	1.80%	20.00%	20.50%	NA
Indica II	465	62.60%	1.30%	14.62%	21.51%	NA
Indica III	913	68.60%	2.60%	15.22%	13.58%	NA
Indica Intermediate	786	65.00%	1.10%	15.14%	18.70%	NA
Temperate Japonica	767	85.00%	1.70%	2.09%	11.21%	NA
Tropical Japonica	504	95.20%	0.40%	1.19%	3.17%	NA
Japonica Intermediate	241	93.40%	0.80%	2.07%	3.73%	NA
VI/Aromatic	96	90.60%	2.10%	4.17%	3.12%	NA
Intermediate	90	86.70%	0.00%	4.44%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712960415	T -> DEL	N	N	silent_mutation	Average:6.357; most accessible tissue: Zhenshan97 flag leaf, score: 9.474	N	N	N	N
vg0712960415	T -> C	LOC_Os07g22970.1	downstream_gene_variant ; 1990.0bp to feature; MODIFIER	silent_mutation	Average:6.357; most accessible tissue: Zhenshan97 flag leaf, score: 9.474	N	N	N	N
vg0712960415	T -> C	LOC_Os07g22970-LOC_Os07g22980	intergenic_region ; MODIFIER	silent_mutation	Average:6.357; most accessible tissue: Zhenshan97 flag leaf, score: 9.474	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712960415	3.32E-06	3.32E-06	mr1015_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