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Detailed information for vg1114274296:

Variant ID: vg1114274296 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14274296
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCTGGAATCATCCCTAAGGATTGCATCAATTGTAAATCAGAGCCAGCCTGATCAAGAAGCGAAGCCAGGGAACCGTGTTTCCCCAAGACACCACCCAT[C/T]
AGCACATCCTTCTTACTAGAATTGGCATGAACCATCATCCCTTGTGCCTGCTGCTCGAGCTGTTCATCAACATTCAGATCTCCAGTCTGTTCGTGGCCTT

Reverse complement sequence

AAGGCCACGAACAGACTGGAGATCTGAATGTTGATGAACAGCTCGAGCAGCAGGCACAAGGGATGATGGTTCATGCCAATTCTAGTAAGAAGGATGTGCT[G/A]
ATGGGTGGTGTCTTGGGGAAACACGGTTCCCTGGCTTCGCTTCTTGATCAGGCTGGCTCTGATTTACAATTGATGCAATCCTTAGGGATGATTCCAGCAA

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	58.50%	4.30%	2.52%	34.72%	NA
All Indica	2759	40.40%	0.40%	2.03%	57.19%	NA
All Japonica	1512	82.40%	12.60%	3.84%	1.12%	NA
Aus	269	91.40%	0.00%	0.00%	8.55%	NA
Indica I	595	43.50%	1.20%	0.67%	54.62%	NA
Indica II	465	14.60%	0.00%	2.80%	82.58%	NA
Indica III	913	54.40%	0.00%	1.20%	44.36%	NA
Indica Intermediate	786	36.90%	0.50%	3.56%	59.03%	NA
Temperate Japonica	767	72.50%	20.20%	6.65%	0.65%	NA
Tropical Japonica	504	97.60%	0.20%	0.20%	1.98%	NA
Japonica Intermediate	241	82.20%	14.50%	2.49%	0.83%	NA
VI/Aromatic	96	95.80%	0.00%	4.17%	0.00%	NA
Intermediate	90	73.30%	0.00%	1.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1114274296	C -> T	LOC_Os11g25050.1	synonymous_variant ; p.Leu224Leu; LOW	synonymous_codon	Average:11.404; most accessible tissue: Callus, score: 64.151	N	N	N	N
vg1114274296	C -> DEL	LOC_Os11g25050.1	N	frameshift_variant	Average:11.404; most accessible tissue: Callus, score: 64.151	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114274296	1.74E-07	NA	mr1137	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
vg1114274296	NA	6.57E-08	mr1424	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
vg1114274296	NA	9.17E-06	mr1564	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
vg1114274296	1.54E-07	NA	mr1617	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
vg1114274296	NA	2.64E-06	mr1884	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