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Detailed information for vg0700217233:

Variant ID: vg0700217233 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 217233
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCACTAACACACTTATGACCTCTATATAACTATATAACTATGATGCACACAACCAAAACACACACACATCCAAAAGTTTACAAGAAAAGGAAGCAGAT[G/A]
AAGTATTACGAACCATCACTTCTAAGATTAGATCGCCACCCATATTTTTGAGTAAAAGAATTTCCTTGGCCGCTTAGTCTAAGCATAGACACCCCACAAT

Reverse complement sequence

ATTGTGGGGTGTCTATGCTTAGACTAAGCGGCCAAGGAAATTCTTTTACTCAAAAATATGGGTGGCGATCTAATCTTAGAAGTGATGGTTCGTAATACTT[C/T]
ATCTGCTTCCTTTTCTTGTAAACTTTTGGATGTGTGTGTGTTTTGGTTGTGTGCATCATAGTTATATAGTTATATAGAGGTCATAAGTGTGTTAGTGGTT

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	98.10%	1.70%	0.25%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	94.10%	5.10%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.90%	1.60%	0.52%	0.00%	NA
Tropical Japonica	504	96.40%	3.00%	0.60%	0.00%	NA
Japonica Intermediate	241	77.20%	20.70%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0700217233	G -> A	LOC_Os07g01340.1	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
vg0700217233	5.16E-06	5.16E-06	mr1750	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
vg0700217233	1.17E-06	1.17E-06	mr1987	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