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Detailed information for vg1123452531:

Variant ID: vg1123452531 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23452531
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATTCAAAAATATGCGCAAATTAAATGCTGGTAAAATGCACAAGTGTTGCAATATAATGGTACACAAAATTCCCGCAAACAATTCCAGTATATACTATG[A/C]
AATTCTATTCATTTTACCGCAACGATATTAATTAAAAGTAATAAAAGCATCACAAATAATCAATAATCGTAAATGCGATAGATAAATTTCATAATCATAT

Reverse complement sequence

ATATGATTATGAAATTTATCTATCGCATTTACGATTATTGATTATTTGTGATGCTTTTATTACTTTTAATTAATATCGTTGCGGTAAAATGAATAGAATT[T/G]
CATAGTATATACTGGAATTGTTTGCGGGAATTTTGTGTACCATTATATTGCAACACTTGTGCATTTTACCAGCATTTAATTTGCGCATATTTTTGAATAA

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	34.80%	15.00%	3.75%	46.45%	NA
All Indica	2759	24.40%	17.50%	5.65%	52.41%	NA
All Japonica	1512	51.90%	3.40%	0.86%	43.85%	NA
Aus	269	27.50%	59.90%	1.12%	11.52%	NA
Indica I	595	36.50%	6.10%	8.57%	48.91%	NA
Indica II	465	9.90%	16.60%	1.29%	72.26%	NA
Indica III	913	20.40%	26.60%	7.67%	45.35%	NA
Indica Intermediate	786	28.50%	16.30%	3.69%	51.53%	NA
Temperate Japonica	767	77.40%	0.00%	0.39%	22.16%	NA
Tropical Japonica	504	20.60%	9.70%	1.59%	68.06%	NA
Japonica Intermediate	241	35.70%	1.20%	0.83%	62.24%	NA
VI/Aromatic	96	75.00%	3.10%	0.00%	21.88%	NA
Intermediate	90	44.40%	12.20%	5.56%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123452531	A -> DEL	N	N	silent_mutation	Average:26.874; most accessible tissue: Callus, score: 51.884	N	N	N	N
vg1123452531	A -> C	LOC_Os11g39400.1	upstream_gene_variant ; 1423.0bp to feature; MODIFIER	silent_mutation	Average:26.874; most accessible tissue: Callus, score: 51.884	N	N	N	N
vg1123452531	A -> C	LOC_Os11g39410.1	downstream_gene_variant ; 3639.0bp to feature; MODIFIER	silent_mutation	Average:26.874; most accessible tissue: Callus, score: 51.884	N	N	N	N
vg1123452531	A -> C	LOC_Os11g39390-LOC_Os11g39400	intergenic_region ; MODIFIER	silent_mutation	Average:26.874; most accessible tissue: Callus, score: 51.884	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123452531	NA	7.69E-06	mr1703_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