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Detailed information for vg0404665746:

Variant ID: vg0404665746 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4665746
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: 123. )

Flanking Sequence (100 bp) in Reference Genome:

ACCGCTAAAACAATCCGAATAGATTTTAGCATGGCGGCTGGCGAGAAAGTTTCATCATAATCAACACCTTGAATTTGTCTGAAACCTTTCACCACCAATC[G/A]
TGCCTTGTAGATGTAAACATTTCCATCTACATCTGTCTTTTTCTTAAAGACCTATTTGCACTCAATGGCTTTTACACCATCAGGTGGATCAACCAAGTTC

Reverse complement sequence

GAACTTGGTTGATCCACCTGATGGTGTAAAAGCCATTGAGTGCAAATAGGTCTTTAAGAAAAAGACAGATGTAGATGGAAATGTTTACATCTACAAGGCA[C/T]
GATTGGTGGTGAAAGGTTTCAGACAAATTCAAGGTGTTGATTATGATGAAACTTTCTCGCCAGCCGCCATGCTAAAATCTATTCGGATTGTTTTAGCGGT

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	96.40%	3.40%	0.11%	0.15%	NA
All Indica	2759	96.00%	3.60%	0.18%	0.14%	NA
All Japonica	1512	96.20%	3.80%	0.00%	0.00%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	97.80%	1.20%	0.84%	0.17%	NA
Indica II	465	91.40%	8.60%	0.00%	0.00%	NA
Indica III	913	99.30%	0.50%	0.00%	0.11%	NA
Indica Intermediate	786	93.60%	6.10%	0.00%	0.25%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	84.60%	15.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	96.70%	2.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404665746	G -> DEL	LOC_Os04g08580.1	N	frameshift_variant	Average:16.983; most accessible tissue: Callus, score: 29.3	N	N	N	N
vg0404665746	G -> A	LOC_Os04g08580.1	N	stop_gained	Average:16.983; most accessible tissue: Callus, score: 29.3	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404665746	NA	2.00E-06	mr1560	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