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Detailed information for vg0202449000:

Variant ID: vg0202449000 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2449000
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAACTTGATTCTTTAACTAAAATATAAGTGTTAATTTTAAAGGGCTACAGTTCAAGAATGTCCAAATCAGATAACATAATGCAATGTGCTATATATCCT[A/G]
AGTGTGAGGTAATAAAAATAAATCAGATAAAACCATGGAAACTTTTGTTTGCTGAGAAAACCAACAATTCAAAATAGCATCCTTAAGCATTCATATCATC

Reverse complement sequence

GATGATATGAATGCTTAAGGATGCTATTTTGAATTGTTGGTTTTCTCAGCAAACAAAAGTTTCCATGGTTTTATCTGATTTATTTTTATTACCTCACACT[T/C]
AGGATATATAGCACATTGCATTATGTTATCTGATTTGGACATTCTTGAACTGTAGCCCTTTAAAATTAACACTTATATTTTAGTTAAAGAATCAAGTTTT

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	84.60%	11.50%	0.17%	3.75%	NA
All Indica	2759	85.90%	11.20%	0.14%	2.75%	NA
All Japonica	1512	99.10%	0.40%	0.00%	0.46%	NA
Aus	269	17.50%	80.30%	0.00%	2.23%	NA
Indica I	595	85.90%	13.90%	0.17%	0.00%	NA
Indica II	465	96.10%	2.60%	0.00%	1.29%	NA
Indica III	913	81.50%	14.50%	0.33%	3.72%	NA
Indica Intermediate	786	85.10%	10.30%	0.00%	4.58%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.00%	0.20%	NA
Japonica Intermediate	241	97.10%	0.40%	0.00%	2.49%	NA
VI/Aromatic	96	9.40%	2.10%	3.12%	85.42%	NA
Intermediate	90	81.10%	11.10%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0202449000	A -> G	LOC_Os02g05130.1	upstream_gene_variant ; 2316.0bp to feature; MODIFIER	silent_mutation	Average:51.956; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0202449000	A -> G	LOC_Os02g05120.1	downstream_gene_variant ; 3285.0bp to feature; MODIFIER	silent_mutation	Average:51.956; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0202449000	A -> G	LOC_Os02g05120-LOC_Os02g05130	intergenic_region ; MODIFIER	silent_mutation	Average:51.956; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0202449000	A -> DEL	N	N	silent_mutation	Average:51.956; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202449000	NA	8.25E-08	mr1654_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