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Detailed information for vg0201148482:

Variant ID: vg0201148482 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 1148482
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTTCCTGTATTAATTGAACAACCGTGTTTCTTCTTAATTAGTTAGTTGAAACACACTTGTATCAAACAACTGTAAGAATATTCATAAGTAGGAGTAGT[A/G]
CCTTGCTCTTCCATGCATAGCTACTTGCTGTAATTAATTTCCTGTATTAATTGAACAACCGTGTTTCTTCTTAATTAGTTGAAACGTGCACGCTTGTATA

Reverse complement sequence

TATACAAGCGTGCACGTTTCAACTAATTAAGAAGAAACACGGTTGTTCAATTAATACAGGAAATTAATTACAGCAAGTAGCTATGCATGGAAGAGCAAGG[T/C]
ACTACTCCTACTTATGAATATTCTTACAGTTGTTTGATACAAGTGTGTTTCAACTAACTAATTAAGAAGAAACACGGTTGTTCAATTAATACAGGAAATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.90%	12.80%	0.30%	0.00%	NA
All Indica	2759	77.90%	21.70%	0.36%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	97.00%	1.50%	1.49%	0.00%	NA
Indica I	595	97.60%	2.00%	0.34%	0.00%	NA
Indica II	465	88.80%	11.00%	0.22%	0.00%	NA
Indica III	913	56.40%	43.20%	0.44%	0.00%	NA
Indica Intermediate	786	81.40%	18.20%	0.38%	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	100.00%	0.00%	0.00%	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
vg0201148482	A -> G	LOC_Os02g02940.1	upstream_gene_variant ; 3323.0bp to feature; MODIFIER	silent_mutation	Average:56.0; most accessible tissue: Minghui63 root, score: 83.674	N	N	N	N
vg0201148482	A -> G	LOC_Os02g02940.2	upstream_gene_variant ; 3366.0bp to feature; MODIFIER	silent_mutation	Average:56.0; most accessible tissue: Minghui63 root, score: 83.674	N	N	N	N
vg0201148482	A -> G	LOC_Os02g02930.1	intron_variant ; MODIFIER	silent_mutation	Average:56.0; most accessible tissue: Minghui63 root, score: 83.674	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0201148482	4.04E-06	NA	mr1854	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