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Detailed information for vg0113766179:

Variant ID: vg0113766179 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13766179
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: 61. )

Flanking Sequence (100 bp) in Reference Genome:

GCAATGGGATGAAGCAGAACCGGACATCTATAAGGACCCAAATCCTGCAAAGGACCCTGTTGAGGAGACCCTCGTGAATGACACGGCCAAAGATAAGTCT[G/A]
AAGTGCCTAGAGTACTCAGAAGCCACGACTCCAAGAAAAAGGATGAACACAAGGAGAAGTACATGGTAAGCGTCTTCAAGGGGGCAAGGAAAGAGCACTA

Reverse complement sequence

TAGTGCTCTTTCCTTGCCCCCTTGAAGACGCTTACCATGTACTTCTCCTTGTGTTCATCCTTTTTCTTGGAGTCGTGGCTTCTGAGTACTCTAGGCACTT[C/T]
AGACTTATCTTTGGCCGTGTCATTCACGAGGGTCTCCTCAACAGGGTCCTTTGCAGGATTTGGGTCCTTATAGATGTCCGGTTCTGCTTCATCCCATTGC

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	48.90%	14.30%	1.54%	35.25%	NA
All Indica	2759	28.70%	14.20%	2.32%	54.84%	NA
All Japonica	1512	95.00%	2.60%	0.20%	2.25%	NA
Aus	269	3.00%	87.00%	0.37%	9.67%	NA
Indica I	595	30.90%	21.50%	1.01%	46.55%	NA
Indica II	465	30.10%	1.30%	1.72%	66.88%	NA
Indica III	913	26.40%	13.30%	1.64%	58.71%	NA
Indica Intermediate	786	28.80%	17.30%	4.45%	49.49%	NA
Temperate Japonica	767	98.30%	1.30%	0.39%	0.00%	NA
Tropical Japonica	504	88.90%	5.20%	0.00%	5.95%	NA
Japonica Intermediate	241	97.10%	1.20%	0.00%	1.66%	NA
VI/Aromatic	96	29.20%	2.10%	2.08%	66.67%	NA
Intermediate	90	54.40%	10.00%	3.33%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113766179	G -> A	LOC_Os01g24420.1	missense_variant ; p.Glu71Lys; MODERATE	nonsynonymous_codon ; E71K	Average:27.272; most accessible tissue: Callus, score: 74.166	unknown	unknown	DELETERIOUS	0.00
vg0113766179	G -> DEL	LOC_Os01g24420.1	N	frameshift_variant	Average:27.272; most accessible tissue: Callus, score: 74.166	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113766179	NA	4.33E-09	mr1028	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
vg0113766179	6.57E-06	1.98E-06	mr1030	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
vg0113766179	NA	9.88E-08	mr1126	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
vg0113766179	NA	2.13E-07	mr1190	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
vg0113766179	NA	2.88E-07	mr1193	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
vg0113766179	5.55E-06	NA	mr1206	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
vg0113766179	NA	1.34E-06	mr1245	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
vg0113766179	NA	1.56E-08	mr1369	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
vg0113766179	NA	1.57E-07	mr1445	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
vg0113766179	NA	1.14E-09	mr1453	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
vg0113766179	NA	1.69E-06	mr1516	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
vg0113766179	NA	5.35E-10	mr1574	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
vg0113766179	NA	2.54E-08	mr1585	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
vg0113766179	NA	1.83E-07	mr1652	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
vg0113766179	NA	6.46E-07	mr1665	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
vg0113766179	NA	1.70E-10	mr1866	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
vg0113766179	NA	2.51E-06	mr1950	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