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Detailed information for vg0418867182:

Variant ID: vg0418867182 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 18867182
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATATCAAAAATTGACAGCCGATGATTTTTAACGGTTATTTTATTTGGACGAGGTCTGGCCGAATGTTTTTATTCTTCTACTTAATTGAATTCGGTTGTT[C/A]
AATGGTTAATCAGGTTATTATCAGAGAATATATGGGCAAGTGCTTCTCCTGAATGTGATGCATGCATATATGGTTTAATTCCAGTTTTACTTTGCCTCCT

Reverse complement sequence

AGGAGGCAAAGTAAAACTGGAATTAAACCATATATGCATGCATCACATTCAGGAGAAGCACTTGCCCATATATTCTCTGATAATAACCTGATTAACCATT[G/T]
AACAACCGAATTCAATTAAGTAGAAGAATAAAAACATTCGGCCAGACCTCGTCCAAATAAAATAACCGTTAAAAATCATCGGCTGTCAATTTTTGATATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.80%	3.20%	0.93%	17.10%	NA
All Indica	2759	73.90%	0.50%	0.72%	24.90%	NA
All Japonica	1512	89.70%	8.70%	1.46%	0.13%	NA
Aus	269	57.60%	0.00%	0.74%	41.64%	NA
Indica I	595	60.30%	0.00%	1.51%	38.15%	NA
Indica II	465	90.30%	1.70%	0.43%	7.53%	NA
Indica III	913	71.60%	0.20%	0.33%	27.82%	NA
Indica Intermediate	786	77.00%	0.50%	0.76%	21.76%	NA
Temperate Japonica	767	98.80%	0.00%	1.04%	0.13%	NA
Tropical Japonica	504	71.80%	25.80%	2.18%	0.20%	NA
Japonica Intermediate	241	97.90%	0.80%	1.24%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	88.90%	6.70%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0418867182	C -> DEL	N	N	silent_mutation	Average:53.738; most accessible tissue: Zhenshan97 flower, score: 71.688	N	N	N	N
vg0418867182	C -> A	LOC_Os04g31550.1	upstream_gene_variant ; 2237.0bp to feature; MODIFIER	silent_mutation	Average:53.738; most accessible tissue: Zhenshan97 flower, score: 71.688	N	N	N	N
vg0418867182	C -> A	LOC_Os04g31540.1	downstream_gene_variant ; 3859.0bp to feature; MODIFIER	silent_mutation	Average:53.738; most accessible tissue: Zhenshan97 flower, score: 71.688	N	N	N	N
vg0418867182	C -> A	LOC_Os04g31540-LOC_Os04g31550	intergenic_region ; MODIFIER	silent_mutation	Average:53.738; most accessible tissue: Zhenshan97 flower, score: 71.688	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0418867182	9.28E-07	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
vg0418867182	NA	3.49E-08	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
vg0418867182	3.28E-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