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Detailed information for vg1123494495:

Variant ID: vg1123494495 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23494495
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.54, T: 0.48, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

CGCAGGAAGCAGATAGCCTACAAGTGAAGACATGCCTTGAAATAGCATTAAGATGTATTGATAAAGACCGAGCAAAAAGACCTACTATAAGCGATATTGT[T/C]
GATAAAATGAATGAGATCGATACCCTAAAAATGTCACTTCTAAGCAAGGTATATTATCTCCAAACTTGTTTGGTTTCGTACTACACCAAAATAATGCCAA

Reverse complement sequence

TTGGCATTATTTTGGTGTAGTACGAAACCAAACAAGTTTGGAGATAATATACCTTGCTTAGAAGTGACATTTTTAGGGTATCGATCTCATTCATTTTATC[A/G]
ACAATATCGCTTATAGTAGGTCTTTTTGCTCGGTCTTTATCAATACATCTTAATGCTATTTCAAGGCATGTCTTCACTTGTAGGCTATCTGCTTCCTGCG

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	24.50%	24.20%	0.15%	51.14%	NA
All Indica	2759	29.40%	12.60%	0.18%	57.77%	NA
All Japonica	1512	13.90%	45.90%	0.13%	40.08%	NA
Aus	269	14.10%	27.50%	0.00%	58.36%	NA
Indica I	595	36.60%	20.50%	0.00%	42.86%	NA
Indica II	465	12.70%	18.10%	0.43%	68.82%	NA
Indica III	913	34.50%	1.10%	0.00%	64.40%	NA
Indica Intermediate	786	27.90%	16.90%	0.38%	54.83%	NA
Temperate Japonica	767	12.30%	70.00%	0.13%	17.60%	NA
Tropical Japonica	504	17.10%	14.50%	0.20%	68.25%	NA
Japonica Intermediate	241	12.40%	34.90%	0.00%	52.70%	NA
VI/Aromatic	96	76.00%	8.30%	0.00%	15.62%	NA
Intermediate	90	30.00%	20.00%	0.00%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123494495	T -> DEL	LOC_Os11g39450.1	N	frameshift_variant	Average:30.957; most accessible tissue: Callus, score: 84.237	N	N	N	N
vg1123494495	T -> C	LOC_Os11g39450.1	synonymous_variant ; p.Val303Val; LOW	synonymous_codon	Average:30.957; most accessible tissue: Callus, score: 84.237	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123494495	NA	1.89E-06	mr1942	Ind_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
vg1123494495	4.79E-06	NA	mr1228_2	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