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Detailed information for vg0113185147:

Variant ID: vg0113185147 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13185147
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGACGCAATTGACGCAGAATTAGCCTCACTTTACAAAAGAGATGTATTCTCGGCTGTAATGCCTACTCCTCGTGGTATCTTTCCTGTGGGATACAAATG[G/A]
GTTTTCGTCCGGAAAAGGAATGAAATTAACAAGGTGGTGAGATATAAAGCAAGGCTTGTAGCACAAGGTTTTACGCAAAAACCTGGTGTTGATTTCAACG

Reverse complement sequence

CGTTGAAATCAACACCAGGTTTTTGCGTAAAACCTTGTGCTACAAGCCTTGCTTTATATCTCACCACCTTGTTAATTTCATTCCTTTTCCGGACGAAAAC[C/T]
CATTTGTATCCCACAGGAAAGATACCACGAGGAGTAGGCATTACAGCCGAGAATACATCTCTTTTGTAAAGTGAGGCTAATTCTGCGTCAATTGCGTCTT

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	33.90%	0.90%	18.75%	46.40%	NA
All Indica	2759	3.40%	1.60%	25.08%	69.99%	NA
All Japonica	1512	96.40%	0.00%	1.46%	2.12%	NA
Aus	269	0.70%	0.00%	51.67%	47.58%	NA
Indica I	595	3.00%	2.40%	15.29%	79.33%	NA
Indica II	465	4.10%	1.50%	20.22%	74.19%	NA
Indica III	913	2.10%	1.40%	33.63%	62.87%	NA
Indica Intermediate	786	4.70%	1.10%	25.45%	68.70%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	93.50%	0.00%	3.77%	2.78%	NA
Japonica Intermediate	241	95.40%	0.00%	0.83%	3.73%	NA
VI/Aromatic	96	6.20%	0.00%	18.75%	75.00%	NA
Intermediate	90	50.00%	0.00%	16.67%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113185147	G -> A	LOC_Os01g23470.1	stop_gained ; p.Trp694*; HIGH	stop_gained	Average:5.417; most accessible tissue: Minghui63 flag leaf, score: 7.953	N	N	N	N
vg0113185147	G -> DEL	LOC_Os01g23470.1	N	frameshift_variant	Average:5.417; most accessible tissue: Minghui63 flag leaf, score: 7.953	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113185147	3.27E-06	2.80E-06	mr1731	Ind_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