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Detailed information for vg1112626453:

Variant ID: vg1112626453 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12626453
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, C: 0.18, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

TACGACCCTAGAGCTATACAATATTATTAATCAAGGCCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGAATCAGACCGAACTGGCAACC[T/C]
GACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTTGTTAAGCAGGTTTTAAGAATTAAAACACTAACTTGGGTACAT

Reverse complement sequence

ATGTACCCAAGTTAGTGTTTTAATTCTTAAAACCTGCTTAACAACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGTC[A/G]
GGTTGCCAGTTCGGTCTGATTCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGGCCTTGATTAATAATATTGTATAGCTCTAGGGTCGTA

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	64.60%	34.60%	0.80%	0.00%	NA
All Indica	2759	96.20%	2.60%	1.23%	0.00%	NA
All Japonica	1512	5.00%	95.00%	0.00%	0.00%	NA
Aus	269	97.40%	1.10%	1.49%	0.00%	NA
Indica I	595	96.60%	2.70%	0.67%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	97.00%	1.10%	1.86%	0.00%	NA
Indica Intermediate	786	93.30%	5.20%	1.53%	0.00%	NA
Temperate Japonica	767	3.80%	96.20%	0.00%	0.00%	NA
Tropical Japonica	504	8.10%	91.90%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	57.80%	42.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112626453	T -> C	LOC_Os11g21980.1	intron_variant ; MODIFIER	silent_mutation	Average:20.519; most accessible tissue: Minghui63 root, score: 33.152	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112626453	NA	1.39E-08	mr1595	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
vg1112626453	2.90E-06	2.90E-06	mr1281_2	Ind_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