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Detailed information for vg0417992105:

Variant ID: vg0417992105 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17992105
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGACGCTCTAATAAATTATAGAAATTATGAGAAAAAAATATCAAACTATTGATTTTCATTTAGAATAGTCACCAGTAATTTAAAACATCATATCAAAAT[A/G]
AAATCCCTCTTACCTATATGTACATGCGCCTATCCTCCCCTCATTTTCTCTTTATTTTTTCTTCTTTTTCTAATTAAGGTAGTTATTATGAGATATGCAC

Reverse complement sequence

GTGCATATCTCATAATAACTACCTTAATTAGAAAAAGAAGAAAAAATAAAGAGAAAATGAGGGGAGGATAGGCGCATGTACATATAGGTAAGAGGGATTT[T/C]
ATTTTGATATGATGTTTTAAATTACTGGTGACTATTCTAAATGAAAATCAATAGTTTGATATTTTTTTCTCATAATTTCTATAATTTATTAGAGCGTCAC

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	57.90%	2.10%	2.56%	37.41%	NA
All Indica	2759	56.40%	0.10%	2.86%	40.67%	NA
All Japonica	1512	52.10%	6.40%	1.39%	40.08%	NA
Aus	269	97.00%	0.00%	1.86%	1.12%	NA
Indica I	595	92.80%	0.00%	0.17%	7.06%	NA
Indica II	465	33.10%	0.00%	3.87%	63.01%	NA
Indica III	913	41.10%	0.00%	5.04%	53.89%	NA
Indica Intermediate	786	60.40%	0.30%	1.78%	37.53%	NA
Temperate Japonica	767	66.60%	0.10%	0.52%	32.72%	NA
Tropical Japonica	504	34.50%	17.70%	2.38%	45.44%	NA
Japonica Intermediate	241	42.70%	2.90%	2.07%	52.28%	NA
VI/Aromatic	96	79.20%	0.00%	12.50%	8.33%	NA
Intermediate	90	61.10%	2.20%	4.44%	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
vg0417992105	A -> DEL	N	N	silent_mutation	Average:6.371; most accessible tissue: Callus, score: 25.416	N	N	N	N
vg0417992105	A -> G	LOC_Os04g30150.1	upstream_gene_variant ; 2232.0bp to feature; MODIFIER	silent_mutation	Average:6.371; most accessible tissue: Callus, score: 25.416	N	N	N	N
vg0417992105	A -> G	LOC_Os04g30150-LOC_Os04g30160	intergenic_region ; MODIFIER	silent_mutation	Average:6.371; most accessible tissue: Callus, score: 25.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417992105	2.11E-07	2.15E-06	mr1925	Jap_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
vg0417992105	6.15E-07	NA	mr1993_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