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Detailed information for vg0517141450:

Variant ID: vg0517141450 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17141450
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: 107. )

Flanking Sequence (100 bp) in Reference Genome:

ATCAGCATCTGAATATCCACTTAAGCATATAGAAGATGAAGTAGAATACAAAATTCCAAACTCAAGTGTATGATTCAAATACCTCATTATTTGCTTGACC[G/A]
CTTGACGATGTGAAGCACGAGGAGAAGCTTGAAAGCGCGCACACAAACACACAGCAAATTGTATGTCTGACCTAGAAGTAGTTAGATACAATAAAGATCC

Reverse complement sequence

GGATCTTTATTGTATCTAACTACTTCTAGGTCAGACATACAATTTGCTGTGTGTTTGTGTGCGCGCTTTCAAGCTTCTCCTCGTGCTTCACATCGTCAAG[C/T]
GGTCAAGCAAATAATGAGGTATTTGAATCATACACTTGAGTTTGGAATTTTGTATTCTACTTCATCTTCTATATGCTTAAGTGGATATTCAGATGCTGAT

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	41.30%	2.80%	12.97%	43.00%	NA
All Indica	2759	15.30%	4.10%	14.32%	66.29%	NA
All Japonica	1512	91.40%	0.20%	0.60%	7.80%	NA
Aus	269	2.20%	4.50%	74.35%	18.96%	NA
Indica I	595	10.80%	5.50%	13.11%	70.59%	NA
Indica II	465	7.10%	2.40%	23.01%	67.53%	NA
Indica III	913	22.30%	4.70%	11.94%	61.01%	NA
Indica Intermediate	786	15.30%	3.40%	12.85%	68.45%	NA
Temperate Japonica	767	97.10%	0.00%	0.52%	2.35%	NA
Tropical Japonica	504	81.20%	0.60%	0.79%	17.46%	NA
Japonica Intermediate	241	94.60%	0.00%	0.41%	4.98%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	53.30%	1.10%	7.78%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517141450	G -> DEL	LOC_Os05g29174.1	N	frameshift_variant	Average:8.585; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg0517141450	G -> A	LOC_Os05g29174.1	missense_variant ; p.Ala113Val; MODERATE	nonsynonymous_codon ; A113V	Average:8.585; most accessible tissue: Zhenshan97 root, score: 12.891	possibly damaging	1.773	TOLERATED	0.12

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517141450	4.87E-06	NA	mr1754	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
vg0517141450	8.84E-06	NA	mr1754	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