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Detailed information for vg0714215236:

Variant ID: vg0714215236 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14215236
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTTCGCCGCCGGCCGCCGTAGCTCACCGTCGCCGGTCATCCCGAGCCGCCGCCGACGCCCCTTCGTCGCCGGCCGTCGTCGGTCGTCGTTTGGCACGAG[G/A]
GTGAGTACCGTTGGGTTCGTCGCGTCGTCCTCTACGTGTACATGCCCTCCAATTTCGCAGCCGACCATCCAATCTCCGGCGAGGTCGCCATCTTGGTCCG

Reverse complement sequence

CGGACCAAGATGGCGACCTCGCCGGAGATTGGATGGTCGGCTGCGAAATTGGAGGGCATGTACACGTAGAGGACGACGCGACGAACCCAACGGTACTCAC[C/T]
CTCGTGCCAAACGACGACCGACGACGGCCGGCGACGAAGGGGCGTCGGCGGCGGCTCGGGATGACCGGCGACGGTGAGCTACGGCGGCCGGCGGCGAAGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.80%	0.30%	3.98%	16.00%	NA
All Indica	2759	85.10%	0.10%	5.00%	9.75%	NA
All Japonica	1512	70.00%	0.40%	1.79%	27.84%	NA
Aus	269	75.10%	0.40%	5.95%	18.59%	NA
Indica I	595	97.30%	0.00%	1.18%	1.51%	NA
Indica II	465	92.00%	0.00%	3.66%	4.30%	NA
Indica III	913	70.10%	0.10%	8.87%	20.92%	NA
Indica Intermediate	786	89.30%	0.30%	4.20%	6.23%	NA
Temperate Japonica	767	87.00%	0.50%	0.91%	11.60%	NA
Tropical Japonica	504	43.70%	0.00%	2.38%	53.97%	NA
Japonica Intermediate	241	71.00%	0.80%	3.32%	24.90%	NA
VI/Aromatic	96	86.50%	3.10%	6.25%	4.17%	NA
Intermediate	90	85.60%	0.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714215236	G -> DEL	N	N	silent_mutation	Average:31.396; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N
vg0714215236	G -> A	LOC_Os07g24970.1	downstream_gene_variant ; 2435.0bp to feature; MODIFIER	silent_mutation	Average:31.396; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N
vg0714215236	G -> A	LOC_Os07g24960-LOC_Os07g24970	intergenic_region ; MODIFIER	silent_mutation	Average:31.396; most accessible tissue: Zhenshan97 flag leaf, score: 67.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714215236	1.12E-06	1.12E-06	mr1973	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