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Detailed information for vg0700240229:

Variant ID: vg0700240229 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 240229
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTCTGGTTTTGTGATTCGGGGGGTAATTCATACTGTCACAATAGTTCGGAGGGGGGTAATTCGTACTTTTTCCTATTTTTTATAGTTAACTATTGTAT[G/A]
AATGGACTATTAGATTAGCTATAAATGATTTGGAGCTAATATTTGGCTATACTATTAAACTTGCTCTTAGAATTAAAAAAGAAATGTACTCCATTATCAT

Reverse complement sequence

ATGATAATGGAGTACATTTCTTTTTTAATTCTAAGAGCAAGTTTAATAGTATAGCCAAATATTAGCTCCAAATCATTTATAGCTAATCTAATAGTCCATT[C/T]
ATACAATAGTTAACTATAAAAAATAGGAAAAAGTACGAATTACCCCCCTCCGAACTATTGTGACAGTATGAATTACCCCCCGAATCACAAAACCAGACAT

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	87.40%	12.00%	0.66%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.07%	0.00%	NA
All Japonica	1512	62.20%	36.00%	1.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	0.60%	0.43%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	37.00%	60.20%	2.74%	0.00%	NA
Tropical Japonica	504	96.60%	3.40%	0.00%	0.00%	NA
Japonica Intermediate	241	70.10%	27.40%	2.49%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	13.30%	2.22%	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
vg0700240229	G -> A	LOC_Os07g01390.1	upstream_gene_variant ; 2233.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700240229	G -> A	LOC_Os07g01370.1	downstream_gene_variant ; 2783.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700240229	G -> A	LOC_Os07g01380.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0700240229	2.56E-06	1.53E-09	mr1977	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
vg0700240229	NA	9.59E-08	mr1977	Jap_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