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Detailed information for vg0128951131:

Variant ID: vg0128951131 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 28951131
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

ATCAGCACGCTGTGCTTGACCTGGGAGAAGGGAAAAAAAAACGCATTTCCATCTTCTAAAAAAAGAAGAAAAAAGAGTGCATTTGCGTACTGCTTGCGGC[G/A]
CCTTGGATTGCCTACCTGGGGTCACAGTTTTCCGTTGTTATGCCTGCCATGAACATTTTTAAGCCATCCACATGACATTATTGGCATAGACATCTAGAAA

Reverse complement sequence

TTTCTAGATGTCTATGCCAATAATGTCATGTGGATGGCTTAAAAATGTTCATGGCAGGCATAACAACGGAAAACTGTGACCCCAGGTAGGCAATCCAAGG[C/T]
GCCGCAAGCAGTACGCAAATGCACTCTTTTTTCTTCTTTTTTTAGAAGATGGAAATGCGTTTTTTTTTCCCTTCTCCCAGGTCAAGCACAGCGTGCTGAT

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	97.80%	2.00%	0.17%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	94.50%	5.00%	0.46%	0.00%	NA
Aus	269	95.90%	4.10%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	97.30%	2.20%	0.52%	0.00%	NA
Tropical Japonica	504	87.90%	11.70%	0.40%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0128951131	G -> A	LOC_Os01g50420.1	upstream_gene_variant ; 3086.0bp to feature; MODIFIER	silent_mutation	Average:68.776; most accessible tissue: Minghui63 root, score: 88.244	N	N	N	N
vg0128951131	G -> A	LOC_Os01g50430.1	upstream_gene_variant ; 1051.0bp to feature; MODIFIER	silent_mutation	Average:68.776; most accessible tissue: Minghui63 root, score: 88.244	N	N	N	N
vg0128951131	G -> A	LOC_Os01g50440.1	upstream_gene_variant ; 4552.0bp to feature; MODIFIER	silent_mutation	Average:68.776; most accessible tissue: Minghui63 root, score: 88.244	N	N	N	N
vg0128951131	G -> A	LOC_Os01g50420-LOC_Os01g50430	intergenic_region ; MODIFIER	silent_mutation	Average:68.776; most accessible tissue: Minghui63 root, score: 88.244	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0128951131	4.82E-06	4.82E-06	mr1438_2	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