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Detailed information for vg0417240491:

Variant ID: vg0417240491 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17240491
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTTGGCATGGGCAGTACTCTTAATGTTTCTTTCTTCCTTTGGCTTTATATATCTTATTATCTATTCAACGACAACTAAAATGATGAATGTTATTGTTT[A/C]
TTATTGCATAGGCTAGACTTGGAATAACATTTTGTGCTTTTATACCAGCTCATATACCGTCATATATACCTCTTTTCACGGTACTTTCTCTAGCAGAGGA

Reverse complement sequence

TCCTCTGCTAGAGAAAGTACCGTGAAAAGAGGTATATATGACGGTATATGAGCTGGTATAAAAGCACAAAATGTTATTCCAAGTCTAGCCTATGCAATAA[T/G]
AAACAATAACATTCATCATTTTAGTTGTCGTTGAATAGATAATAAGATATATAAAGCCAAAGGAAGAAAGAAACATTAAGAGTACTGCCCATGCCAACTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.70%	3.70%	1.46%	3.11%	NA
All Indica	2759	97.60%	0.40%	0.87%	1.09%	NA
All Japonica	1512	87.20%	10.50%	2.31%	0.00%	NA
Aus	269	63.60%	0.00%	2.97%	33.46%	NA
Indica I	595	97.60%	0.00%	2.35%	0.00%	NA
Indica II	465	98.10%	1.30%	0.22%	0.43%	NA
Indica III	913	98.40%	0.10%	0.00%	1.53%	NA
Indica Intermediate	786	96.40%	0.60%	1.15%	1.78%	NA
Temperate Japonica	767	95.20%	2.10%	2.74%	0.00%	NA
Tropical Japonica	504	70.00%	27.60%	2.38%	0.00%	NA
Japonica Intermediate	241	97.50%	1.70%	0.83%	0.00%	NA
VI/Aromatic	96	70.80%	0.00%	1.04%	28.12%	NA
Intermediate	90	95.60%	3.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417240491	A -> C	LOC_Os04g29080.1	downstream_gene_variant ; 3109.0bp to feature; MODIFIER	silent_mutation	Average:40.728; most accessible tissue: Callus, score: 71.88	N	N	N	N
vg0417240491	A -> C	LOC_Os04g29080-LOC_Os04g29090	intergenic_region ; MODIFIER	silent_mutation	Average:40.728; most accessible tissue: Callus, score: 71.88	N	N	N	N
vg0417240491	A -> DEL	N	N	silent_mutation	Average:40.728; most accessible tissue: Callus, score: 71.88	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417240491	2.86E-06	NA	mr1301	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
vg0417240491	9.45E-08	NA	mr1410	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
vg0417240491	NA	9.22E-06	mr1082_2	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
vg0417240491	2.99E-06	NA	mr1410_2	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