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Detailed information for vg0224387072:

Variant ID: vg0224387072 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24387072
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTAAAAAAAGTCAACGGCGTCAAATATTTAGACGGAGGGAGTATAAAATTAGTAATTAAGTAATATTTTCATTTAAAGAAGCTTACACGACTATGAAA[G/A]
TTTAAAGAAGATTACCATACTATTTTTTACTTATCGGGTCTATGCGGGCGGACGGGCGGGCGGTGCACTGCAGCCAGGAGGTTAGGAGGCAGTTCTCTGT

Reverse complement sequence

ACAGAGAACTGCCTCCTAACCTCCTGGCTGCAGTGCACCGCCCGCCCGTCCGCCCGCATAGACCCGATAAGTAAAAAATAGTATGGTAATCTTCTTTAAA[C/T]
TTTCATAGTCGTGTAAGCTTCTTTAAATGAAAATATTACTTAATTACTAATTTTATACTCCCTCCGTCTAAATATTTGACGCCGTTGACTTTTTTTAAAC

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	56.80%	34.10%	1.44%	7.62%	NA
All Indica	2759	59.90%	26.90%	1.74%	11.49%	NA
All Japonica	1512	48.10%	50.20%	0.33%	1.39%	NA
Aus	269	76.20%	15.60%	5.20%	2.97%	NA
Indica I	595	39.20%	26.70%	0.84%	33.28%	NA
Indica II	465	83.90%	12.70%	0.65%	2.80%	NA
Indica III	913	56.70%	32.50%	3.07%	7.67%	NA
Indica Intermediate	786	65.10%	28.80%	1.53%	4.58%	NA
Temperate Japonica	767	35.20%	62.60%	0.52%	1.69%	NA
Tropical Japonica	504	71.20%	27.60%	0.00%	1.19%	NA
Japonica Intermediate	241	40.70%	58.10%	0.41%	0.83%	NA
VI/Aromatic	96	44.80%	43.80%	1.04%	10.42%	NA
Intermediate	90	64.40%	31.10%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224387072	G -> A	LOC_Os02g40270.1	upstream_gene_variant ; 4399.0bp to feature; MODIFIER	silent_mutation	Average:48.865; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0224387072	G -> A	LOC_Os02g40280.1	downstream_gene_variant ; 3659.0bp to feature; MODIFIER	silent_mutation	Average:48.865; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0224387072	G -> A	LOC_Os02g40270-LOC_Os02g40280	intergenic_region ; MODIFIER	silent_mutation	Average:48.865; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0224387072	G -> DEL	N	N	silent_mutation	Average:48.865; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224387072	3.67E-06	NA	mr1189_2	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
vg0224387072	9.62E-06	NA	mr1722_2	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