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Detailed information for vg1121393340:

Variant ID: vg1121393340 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21393340
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTCAAATTTAAAAGTGGTTAAACGAAGGGAGTATGACTAAGGTAATTAATTAAGTACTCCCTCCGTCCCATAATATAAGGGATTTTGAGTTTTTATTTG[C/T,A]
ATTGTTTGACCACTCATCTTATTCAAAAAATTTATGCAAATATAAAAAACGAAAAGTTGTGCTTAAAGTATTTTGGGTAATAAAGTAAGTCAAAAAAAAT

Reverse complement sequence

ATTTTTTTTGACTTACTTTATTACCCAAAATACTTTAAGCACAACTTTTCGTTTTTTATATTTGCATAAATTTTTTGAATAAGATGAGTGGTCAAACAAT[G/A,T]
CAAATAAAAACTCAAAATCCCTTATATTATGGGACGGAGGGAGTACTTAATTAATTACCTTAGTCATACTCCCTTCGTTTAACCACTTTTAAATTTGAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.00%	5.10%	0.23%	23.23%	A: 0.47%
All Indica	2759	57.60%	3.70%	0.25%	37.77%	A: 0.72%
All Japonica	1512	91.30%	5.40%	0.20%	3.04%	NA
Aus	269	92.20%	7.80%	0.00%	0.00%	NA
Indica I	595	65.20%	4.20%	0.17%	29.92%	A: 0.50%
Indica II	465	48.80%	0.00%	0.00%	51.18%	NA
Indica III	913	58.60%	5.00%	0.44%	34.94%	A: 0.99%
Indica Intermediate	786	55.90%	3.80%	0.25%	39.06%	A: 1.02%
Temperate Japonica	767	93.40%	3.40%	0.26%	3.00%	NA
Tropical Japonica	504	86.70%	9.50%	0.00%	3.77%	NA
Japonica Intermediate	241	94.60%	3.30%	0.41%	1.66%	NA
VI/Aromatic	96	72.90%	27.10%	0.00%	0.00%	NA
Intermediate	90	73.30%	12.20%	1.11%	11.11%	A: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121393340	C -> T	LOC_Os11g36320.1	upstream_gene_variant ; 4840.0bp to feature; MODIFIER	silent_mutation	Average:50.624; most accessible tissue: Minghui63 panicle, score: 89.175	N	N	N	N
vg1121393340	C -> T	LOC_Os11g36320-LOC_Os11g36330	intergenic_region ; MODIFIER	silent_mutation	Average:50.624; most accessible tissue: Minghui63 panicle, score: 89.175	N	N	N	N
vg1121393340	C -> A	LOC_Os11g36320.1	upstream_gene_variant ; 4840.0bp to feature; MODIFIER	silent_mutation	Average:50.624; most accessible tissue: Minghui63 panicle, score: 89.175	N	N	N	N
vg1121393340	C -> A	LOC_Os11g36320-LOC_Os11g36330	intergenic_region ; MODIFIER	silent_mutation	Average:50.624; most accessible tissue: Minghui63 panicle, score: 89.175	N	N	N	N
vg1121393340	C -> DEL	N	N	silent_mutation	Average:50.624; most accessible tissue: Minghui63 panicle, score: 89.175	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121393340	1.09E-06	1.09E-06	mr1526	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