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Detailed information for vg0702749068:

Variant ID: vg0702749068 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2749068
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAACGGTTAGGACATACTCATCCAAAAAAAATCAACATAGAAGAAGAATCTGGACAAAAGGATCAAATTCCCTTCTAGGTAAAGTTTTTTTTTGGGACG[G/A]
AGAGAGTAAGTTCTATCTGTTGATACACTAGTTGTCGTCTTTTCGGGTGGCTCCTTCATCCCTGTAAAAACATACTTTTTTTTAGAATTATATAGTACAA

Reverse complement sequence

TTGTACTATATAATTCTAAAAAAAAGTATGTTTTTACAGGGATGAAGGAGCCACCCGAAAAGACGACAACTAGTGTATCAACAGATAGAACTTACTCTCT[C/T]
CGTCCCAAAAAAAAACTTTACCTAGAAGGGAATTTGATCCTTTTGTCCAGATTCTTCTTCTATGTTGATTTTTTTTGGATGAGTATGTCCTAACCGTTTG

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	95.50%	3.00%	1.52%	0.00%	NA
All Indica	2759	99.60%	0.10%	0.25%	0.00%	NA
All Japonica	1512	86.60%	9.10%	4.30%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	0.30%	1.18%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	75.10%	17.50%	7.43%	0.00%	NA
Tropical Japonica	504	99.00%	0.20%	0.79%	0.00%	NA
Japonica Intermediate	241	97.50%	0.80%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0702749068	G -> A	LOC_Os07g05720.1	upstream_gene_variant ; 2145.0bp to feature; MODIFIER	silent_mutation	Average:53.994; most accessible tissue: Callus, score: 73.386	N	N	N	N
vg0702749068	G -> A	LOC_Os07g05710-LOC_Os07g05720	intergenic_region ; MODIFIER	silent_mutation	Average:53.994; most accessible tissue: Callus, score: 73.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702749068	2.10E-06	2.55E-06	mr1875	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