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Detailed information for vg0401578564:

Variant ID: vg0401578564 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1578564
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGGCGAAACATGGGTAACAACATGGAACCCTTCATCCTTTCTATTTACGCTTCTCTCGCCCTTCCTTCTCTTCGCCTTTGCTGACCGTTCGCTTTTCT[G/A]
TGTGCCGGTTGTGTTTGCCGGTACGTCCTCGTCTTTTGAAGGAACTTTTTTCTTCGGCTGCCGTTTTGATCGTCGTGGCGCCGTTTCCTACGAGAAGGTA

Reverse complement sequence

TACCTTCTCGTAGGAAACGGCGCCACGACGATCAAAACGGCAGCCGAAGAAAAAAGTTCCTTCAAAAGACGAGGACGTACCGGCAAACACAACCGGCACA[C/T]
AGAAAAGCGAACGGTCAGCAAAGGCGAAGAGAAGGAAGGGCGAGAGAAGCGTAAATAGAAAGGATGAAGGGTTCCATGTTGTTACCCATGTTTCGCCTAA

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	82.90%	0.80%	5.65%	10.69%	NA
All Indica	2759	79.60%	1.00%	6.81%	12.58%	NA
All Japonica	1512	86.00%	0.70%	4.37%	8.99%	NA
Aus	269	92.90%	0.00%	2.97%	4.09%	NA
Indica I	595	77.30%	0.70%	6.39%	15.63%	NA
Indica II	465	78.50%	1.90%	4.52%	15.05%	NA
Indica III	913	79.00%	0.80%	9.09%	11.17%	NA
Indica Intermediate	786	82.80%	0.90%	5.85%	10.43%	NA
Temperate Japonica	767	93.60%	0.00%	0.91%	5.48%	NA
Tropical Japonica	504	79.00%	1.60%	8.93%	10.52%	NA
Japonica Intermediate	241	76.30%	0.80%	5.81%	17.01%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	84.40%	0.00%	4.44%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401578564	G -> DEL	LOC_Os04g03610.1	N	frameshift_variant	Average:25.357; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0401578564	G -> A	LOC_Os04g03610.1	stop_gained ; p.Gln110*; HIGH	stop_gained	Average:25.357; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401578564	7.61E-07	NA	mr1925	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