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Detailed information for vg1116402406:

Variant ID: vg1116402406 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16402406
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCAGATGTTATTCACCATACAAAATTATAAGCTAGCTAGTCATAGGAGCATGAGTTCACCCACCAGGGTTAATCCTAGTCTTCGTAAATATATACTTC[C/A]
TCCGTTTCATATTATAAGACTTTATAGTATTGTTCACATTCGTATATATGTTAATGAATCTAGACATATATGTGTGCCTAGATTTATTAACATCTATATA

Reverse complement sequence

TATATAGATGTTAATAAATCTAGGCACACATATATGTCTAGATTCATTAACATATATACGAATGTGAACAATACTATAAAGTCTTATAATATGAAACGGA[G/T]
GAAGTATATATTTACGAAGACTAGGATTAACCCTGGTGGGTGAACTCATGCTCCTATGACTAGCTAGCTTATAATTTTGTATGGTGAATAACATCTGACA

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	66.40%	4.10%	21.75%	7.83%	NA
All Indica	2759	51.10%	0.70%	35.30%	12.94%	NA
All Japonica	1512	90.50%	8.70%	0.73%	0.13%	NA
Aus	269	89.60%	0.00%	8.18%	2.23%	NA
Indica I	595	50.40%	0.50%	42.52%	6.55%	NA
Indica II	465	49.20%	0.00%	38.92%	11.83%	NA
Indica III	913	52.60%	0.00%	30.23%	17.20%	NA
Indica Intermediate	786	51.00%	1.90%	33.59%	13.49%	NA
Temperate Japonica	767	83.10%	16.30%	0.52%	0.13%	NA
Tropical Japonica	504	98.40%	0.20%	1.19%	0.20%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	60.40%	38.50%	1.04%	0.00%	NA
Intermediate	90	65.60%	6.70%	22.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116402406	C -> A	LOC_Os11g28480-LOC_Os11g28490	intergenic_region ; MODIFIER	silent_mutation	Average:22.087; most accessible tissue: Callus, score: 45.93	N	N	N	N
vg1116402406	C -> DEL	N	N	silent_mutation	Average:22.087; most accessible tissue: Callus, score: 45.93	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116402406	NA	8.94E-06	mr1565_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
vg1116402406	4.00E-06	4.00E-06	mr1915_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
vg1116402406	8.94E-06	8.94E-06	mr1940_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