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Detailed information for vg1122857696:

Variant ID: vg1122857696 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22857696
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, C: 0.37, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCTGAAATTCCCTTAGGTTTCTCGGAGGCTTTGTCAGGGCGGCGTAAAGGGATAGTAGGATTGGATTCAACTCGAGGTGTCTTCGTAGTAAGGGATCT[T/C]
TGAGCAAAACACTTGGCGATATTGTGTACCTGATATCAACTTTATTGAAGTAGAGGTAGTGGGAGAATCGCTACACCACTGGTCGAAAACCAGGGGTAGT

Reverse complement sequence

ACTACCCCTGGTTTTCGACCAGTGGTGTAGCGATTCTCCCACTACCTCTACTTCAATAAAGTTGATATCAGGTACACAATATCGCCAAGTGTTTTGCTCA[A/G]
AGATCCCTTACTACGAAGACACCTCGAGTTGAATCCAATCCTACTATCCCTTTACGCCGCCCTGACAAAGCCTCCGAGAAACCTAAGGGAATTTCAGCTG

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	44.20%	13.70%	0.34%	41.81%	NA
All Indica	2759	62.60%	9.00%	0.40%	28.02%	NA
All Japonica	1512	18.10%	24.30%	0.00%	57.61%	NA
Aus	269	10.00%	7.80%	0.74%	81.41%	NA
Indica I	595	81.50%	3.90%	0.34%	14.29%	NA
Indica II	465	64.10%	4.50%	0.00%	31.40%	NA
Indica III	913	45.90%	17.90%	0.66%	35.60%	NA
Indica Intermediate	786	66.80%	5.20%	0.38%	27.61%	NA
Temperate Japonica	767	30.10%	35.60%	0.00%	34.29%	NA
Tropical Japonica	504	5.20%	7.90%	0.00%	86.90%	NA
Japonica Intermediate	241	7.10%	22.40%	0.00%	70.54%	NA
VI/Aromatic	96	11.50%	2.10%	1.04%	85.42%	NA
Intermediate	90	53.30%	10.00%	2.22%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122857696	T -> DEL	N	N	silent_mutation	Average:49.082; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg1122857696	T -> C	LOC_Os11g38580.1	upstream_gene_variant ; 4751.0bp to feature; MODIFIER	silent_mutation	Average:49.082; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N
vg1122857696	T -> C	LOC_Os11g38560-LOC_Os11g38580	intergenic_region ; MODIFIER	silent_mutation	Average:49.082; most accessible tissue: Zhenshan97 young leaf, score: 68.794	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122857696	3.48E-08	1.61E-09	mr1955	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
vg1122857696	3.06E-07	3.06E-07	mr1955	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