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Detailed information for vg0817402433:

Variant ID: vg0817402433 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17402433
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: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AGATATTCAGATGCTGATTTTGGAGGTTGTAGAATTGATAGGAAAAGTACTAGTGGAATATGTCATTTTCTTGGTACATCATTGATTGCATGGTCTTCTA[G/A]
GAAACAATCTAGTGTTGCTCAATCAACTACTGAATCTGAATATGTTGCTGCTGCTAGTTGTTGTTCACAGATTCTTTGGCTTTTATCTACTTTGAAAGAT

Reverse complement sequence

ATCTTTCAAAGTAGATAAAAGCCAAAGAATCTGTGAACAACAACTAGCAGCAGCAACATATTCAGATTCAGTAGTTGATTGAGCAACACTAGATTGTTTC[C/T]
TAGAAGACCATGCAATCAATGATGTACCAAGAAAATGACATATTCCACTAGTACTTTTCCTATCAATTCTACAACCTCCAAAATCAGCATCTGAATATCT

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	56.80%	0.70%	6.98%	35.55%	NA
All Indica	2759	28.60%	1.10%	11.78%	58.54%	NA
All Japonica	1512	97.20%	0.00%	0.00%	2.78%	NA
Aus	269	98.50%	0.00%	0.74%	0.74%	NA
Indica I	595	40.80%	0.50%	11.93%	46.72%	NA
Indica II	465	17.40%	2.80%	11.18%	68.60%	NA
Indica III	913	26.60%	0.50%	12.92%	59.91%	NA
Indica Intermediate	786	28.20%	1.10%	10.69%	59.92%	NA
Temperate Japonica	767	98.60%	0.00%	0.00%	1.43%	NA
Tropical Japonica	504	94.40%	0.00%	0.00%	5.56%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	0.00%	3.33%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817402433	G -> A	LOC_Os08g28500.1	missense_variant ; p.Arg931Lys; MODERATE	nonsynonymous_codon ; R931K	Average:9.876; most accessible tissue: Callus, score: 23.626	benign	0.504	TOLERATED	1.00
vg0817402433	G -> DEL	LOC_Os08g28500.1	N	frameshift_variant	Average:9.876; most accessible tissue: Callus, score: 23.626	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817402433	8.81E-07	8.81E-07	mr1361	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
vg0817402433	NA	3.39E-06	mr1496	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251