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Detailed information for vg0405892240:

Variant ID: vg0405892240 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5892240
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.13, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

TAATTGCTGGACTTGAAGTCATAAGTGGGACTAATCAAGATGGTTCGTCACTGTATGTTGTTGGTTTGAAGGACGATAATGAGGTGTGAGATGAAGTGAG[A/G]
GTTACTTTTAAAGGCTAGGCGTTGGAAGGTGTGGAATGTCACTGCCGGAAGATGGAGTGCGAAGACATCCCTTGCTCAGACATTTTTGTTGTACTCAAGT

Reverse complement sequence

ACTTGAGTACAACAAAAATGTCTGAGCAAGGGATGTCTTCGCACTCCATCTTCCGGCAGTGACATTCCACACCTTCCAACGCCTAGCCTTTAAAAGTAAC[T/C]
CTCACTTCATCTCACACCTCATTATCGTCCTTCAAACCAACAACATACAGTGACGAACCATCTTGATTAGTCCCACTTATGACTTCAAGTCCAGCAATTA

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	21.80%	5.30%	0.57%	72.37%	NA
All Indica	2759	2.50%	6.50%	0.62%	90.43%	NA
All Japonica	1512	60.20%	4.40%	0.20%	35.19%	NA
Aus	269	8.90%	0.40%	1.12%	89.59%	NA
Indica I	595	2.00%	0.50%	1.34%	96.13%	NA
Indica II	465	4.50%	9.90%	0.22%	85.38%	NA
Indica III	913	1.20%	10.00%	0.33%	88.50%	NA
Indica Intermediate	786	3.20%	4.80%	0.64%	91.35%	NA
Temperate Japonica	767	66.80%	3.30%	0.13%	29.86%	NA
Tropical Japonica	504	43.70%	5.20%	0.40%	50.79%	NA
Japonica Intermediate	241	73.90%	6.60%	0.00%	19.50%	NA
VI/Aromatic	96	5.20%	1.00%	0.00%	93.75%	NA
Intermediate	90	23.30%	3.30%	4.44%	68.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405892240	A -> DEL	N	N	silent_mutation	Average:8.732; most accessible tissue: Callus, score: 33.112	N	N	N	N
vg0405892240	A -> G	LOC_Os04g10850.1	upstream_gene_variant ; 2482.0bp to feature; MODIFIER	silent_mutation	Average:8.732; most accessible tissue: Callus, score: 33.112	N	N	N	N
vg0405892240	A -> G	LOC_Os04g10870.1	downstream_gene_variant ; 2181.0bp to feature; MODIFIER	silent_mutation	Average:8.732; most accessible tissue: Callus, score: 33.112	N	N	N	N
vg0405892240	A -> G	LOC_Os04g10860.1	intron_variant ; MODIFIER	silent_mutation	Average:8.732; most accessible tissue: Callus, score: 33.112	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405892240	3.07E-06	NA	mr1179	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
vg0405892240	NA	2.63E-08	mr1227	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