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Detailed information for vg0413276176:

Variant ID: vg0413276176 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13276176
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCCCATTGCAGGAGAAATGGTCGGCTGGGGATCATGGGACCGATGTGCGGCCATGCGTTCATCAACCAACCTTCCACCTCCTCTTGCATGCTGAGTTC[A/G]
TAGCTCGATACCCAGAACTCCAGATCTGCAACCTTCGCCTCGGTATCTCTCTTGCTCCTCATCTGACTCCTGTACGTGTGGATGTCCTCCTTGAAACCAA

Reverse complement sequence

TTGGTTTCAAGGAGGACATCCACACGTACAGGAGTCAGATGAGGAGCAAGAGAGATACCGAGGCGAAGGTTGCAGATCTGGAGTTCTGGGTATCGAGCTA[T/C]
GAACTCAGCATGCAAGAGGAGGTGGAAGGTTGGTTGATGAACGCATGGCCGCACATCGGTCCCATGATCCCCAGCCGACCATTTCTCCTGCAATGGGGAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.60%	11.70%	21.01%	33.71%	NA
All Indica	2759	17.90%	8.60%	33.02%	40.52%	NA
All Japonica	1512	64.50%	5.30%	1.19%	29.03%	NA
Aus	269	0.40%	77.70%	19.33%	2.60%	NA
Indica I	595	42.50%	0.00%	23.53%	33.95%	NA
Indica II	465	7.70%	7.30%	33.33%	51.61%	NA
Indica III	913	7.80%	13.90%	45.67%	32.64%	NA
Indica Intermediate	786	17.00%	9.50%	25.32%	48.09%	NA
Temperate Japonica	767	89.00%	8.10%	0.39%	2.48%	NA
Tropical Japonica	504	23.60%	1.00%	2.38%	73.02%	NA
Japonica Intermediate	241	71.80%	5.40%	1.24%	21.58%	NA
VI/Aromatic	96	79.20%	16.70%	2.08%	2.08%	NA
Intermediate	90	44.40%	14.40%	11.11%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413276176	A -> DEL	N	N	silent_mutation	Average:10.648; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg0413276176	A -> G	LOC_Os04g23260.1	upstream_gene_variant ; 349.0bp to feature; MODIFIER	silent_mutation	Average:10.648; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg0413276176	A -> G	LOC_Os04g23270.1	downstream_gene_variant ; 132.0bp to feature; MODIFIER	silent_mutation	Average:10.648; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N
vg0413276176	A -> G	LOC_Os04g23260-LOC_Os04g23270	intergenic_region ; MODIFIER	silent_mutation	Average:10.648; most accessible tissue: Zhenshan97 young leaf, score: 18.248	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413276176	NA	4.93E-15	mr1062	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
vg0413276176	NA	4.22E-13	mr1641_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
vg0413276176	NA	5.10E-14	mr1838_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
vg0413276176	NA	5.15E-08	mr1921_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
vg0413276176	2.39E-06	2.39E-06	mr1927_2	Jap_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