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Detailed information for vg0124656601:

Variant ID: vg0124656601 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24656601
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGCACATCATCCGTGTATGAATCGGTTTTTAAGTTCGCTCAATTTTGGAAATACATATCCATAATTGGAAATCCTTTTTACAAATCTCCTCCTCAGAGC[G/A]
CCTTGTAACCTTACCTTTTCTAAATGGTACACCTTATTTAAGACATTCAGAATAGAAGAAGAGCAGTCGTTGATTGATTGAAAGTGGATTGACGGCATTC

Reverse complement sequence

GAATGCCGTCAATCCACTTTCAATCAATCAACGACTGCTCTTCTTCTATTCTGAATGTCTTAAATAAGGTGTACCATTTAGAAAAGGTAAGGTTACAAGG[C/T]
GCTCTGAGGAGGAGATTTGTAAAAAGGATTTCCAATTATGGATATGTATTTCCAAAATTGAGCGAACTTAAAAACCGATTCATACACGGATGATGTGCCA

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	89.30%	10.50%	0.28%	0.00%	NA
All Indica	2759	82.50%	17.10%	0.33%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	94.80%	3.70%	1.49%	0.00%	NA
Indica I	595	95.80%	4.20%	0.00%	0.00%	NA
Indica II	465	94.00%	5.80%	0.22%	0.00%	NA
Indica III	913	71.20%	28.40%	0.44%	0.00%	NA
Indica Intermediate	786	78.90%	20.60%	0.51%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0124656601	G -> A	LOC_Os01g43180-LOC_Os01g43200	intergenic_region ; MODIFIER	silent_mutation	Average:38.039; most accessible tissue: Zhenshan97 flower, score: 53.595	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124656601	NA	1.85E-07	mr1066	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
vg0124656601	3.94E-07	4.03E-07	mr1438	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
vg0124656601	3.39E-07	5.14E-07	mr1438	Ind_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