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Detailed information for vg0410126465:

Variant ID: vg0410126465 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10126465
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

AGATGGAGTCTAGTGATGAGGCTGCATCCATTTGAAAGAGGACTCCGTGAGCTTTCCATCAAGTACTCATGGGCCGAAAACGCAGGTCGTATGCAGATTC[G/A]
GTAGCCGTTTGAAGTCAGCAGTGTAGCAGGTGGCCGAATCAGATTCCAGCGCTTGGAGGACTTTAACTTGATATCTTGTTGTTCATCCATGATGTGAGCA

Reverse complement sequence

TGCTCACATCATGGATGAACAACAAGATATCAAGTTAAAGTCCTCCAAGCGCTGGAATCTGATTCGGCCACCTGCTACACTGCTGACTTCAAACGGCTAC[C/T]
GAATCTGCATACGACCTGCGTTTTCGGCCCATGAGTACTTGATGGAAAGCTCACGGAGTCCTCTTTCAAATGGATGCAGCCTCATCACTAGACTCCATCT

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	55.20%	12.10%	29.07%	3.60%	NA
All Indica	2759	32.60%	19.10%	46.32%	1.99%	NA
All Japonica	1512	98.40%	0.80%	0.73%	0.07%	NA
Aus	269	29.70%	9.30%	21.93%	39.03%	NA
Indica I	595	30.90%	11.90%	57.14%	0.00%	NA
Indica II	465	29.50%	18.90%	51.40%	0.22%	NA
Indica III	913	36.50%	24.60%	34.50%	4.38%	NA
Indica Intermediate	786	31.20%	18.20%	48.85%	1.78%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	98.80%	0.60%	0.40%	0.20%	NA
Japonica Intermediate	241	93.80%	2.90%	3.32%	0.00%	NA
VI/Aromatic	96	88.50%	1.00%	4.17%	6.25%	NA
Intermediate	90	62.20%	10.00%	24.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410126465	G -> DEL	LOC_Os04g18340.1	N	frameshift_variant	Average:21.671; most accessible tissue: Callus, score: 44.66	N	N	N	N
vg0410126465	G -> A	LOC_Os04g18340.1	stop_gained ; p.Arg292*; HIGH	stop_gained	Average:21.671; most accessible tissue: Callus, score: 44.66	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410126465	6.39E-06	NA	mr1068	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
vg0410126465	9.83E-07	NA	mr1068	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
vg0410126465	8.29E-06	NA	mr1087	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
vg0410126465	4.39E-06	NA	mr1090	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
vg0410126465	5.97E-06	NA	mr1091	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
vg0410126465	2.94E-06	NA	mr1091	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
vg0410126465	3.32E-06	NA	mr1108	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
vg0410126465	6.78E-06	NA	mr1111	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
vg0410126465	7.85E-06	NA	mr1111	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
vg0410126465	7.60E-07	NA	mr1121	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
vg0410126465	2.35E-06	NA	mr1121	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
vg0410126465	3.36E-06	NA	mr1068_2	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
vg0410126465	4.55E-06	NA	mr1068_2	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