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Detailed information for vg1117402464:

Variant ID: vg1117402464 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17402464
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGATCAAATAATTCTGTTAGTCAACACGTTTGACGGGGGTAATTACCATTCTGCCCTTGTTCTCTAGGACGTAGCTGCAACTCCCTACTCATCAGAAAC[C/A]
GCCGTCGACGCCCATGAATGGATCGATCTAGGGTTCATATTACTCTGTCTCAAAATATAGCTATTTCTAGCACAATACCTTGTCCCAAAATGAAACTATT

Reverse complement sequence

AATAGTTTCATTTTGGGACAAGGTATTGTGCTAGAAATAGCTATATTTTGAGACAGAGTAATATGAACCCTAGATCGATCCATTCATGGGCGTCGACGGC[G/T]
GTTTCTGATGAGTAGGGAGTTGCAGCTACGTCCTAGAGAACAAGGGCAGAATGGTAATTACCCCCGTCAAACGTGTTGACTAACAGAATTATTTGATCCT

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	73.70%	3.10%	5.97%	17.29%	NA
All Indica	2759	89.80%	0.00%	1.23%	8.95%	NA
All Japonica	1512	50.50%	9.10%	13.96%	26.52%	NA
Aus	269	42.40%	0.00%	1.49%	56.13%	NA
Indica I	595	92.60%	0.00%	2.86%	4.54%	NA
Indica II	465	84.90%	0.00%	0.86%	14.19%	NA
Indica III	913	91.50%	0.10%	0.88%	7.56%	NA
Indica Intermediate	786	88.50%	0.00%	0.64%	10.81%	NA
Temperate Japonica	767	71.10%	0.30%	13.95%	14.73%	NA
Tropical Japonica	504	28.40%	24.00%	11.71%	35.91%	NA
Japonica Intermediate	241	31.10%	5.80%	18.67%	44.40%	NA
VI/Aromatic	96	61.50%	4.20%	29.17%	5.21%	NA
Intermediate	90	76.70%	3.30%	5.56%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117402464	C -> A	LOC_Os11g29945.1	upstream_gene_variant ; 943.0bp to feature; MODIFIER	silent_mutation	Average:16.398; most accessible tissue: Callus, score: 26.714	N	N	N	N
vg1117402464	C -> A	LOC_Os11g29940.1	downstream_gene_variant ; 509.0bp to feature; MODIFIER	silent_mutation	Average:16.398; most accessible tissue: Callus, score: 26.714	N	N	N	N
vg1117402464	C -> A	LOC_Os11g29950.1	downstream_gene_variant ; 2994.0bp to feature; MODIFIER	silent_mutation	Average:16.398; most accessible tissue: Callus, score: 26.714	N	N	N	N
vg1117402464	C -> A	LOC_Os11g29940-LOC_Os11g29945	intergenic_region ; MODIFIER	silent_mutation	Average:16.398; most accessible tissue: Callus, score: 26.714	N	N	N	N
vg1117402464	C -> DEL	N	N	silent_mutation	Average:16.398; most accessible tissue: Callus, score: 26.714	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117402464	9.90E-07	NA	mr1134_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
vg1117402464	6.27E-06	NA	mr1504_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