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Detailed information for vg1121334009:

Variant ID: vg1121334009 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21334009
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GGAGCCGGGCCCAAAACCGGCACCTATGAGGCCTTTATAACTGGCACCAATGAGTATTTTTGTGGTAGTGATAATATGGAGCGGGAAATTAACATTGCAC[C/T]
GGCGAAATAATACAGGTACAAATAATATGCATCCAAGACTGGTGCTCCCCATAATTATCGATCTTCTTCTCTCGCGATCGTTCAGTACTATTAAGACAGA

Reverse complement sequence

TCTGTCTTAATAGTACTGAACGATCGCGAGAGAAGAAGATCGATAATTATGGGGAGCACCAGTCTTGGATGCATATTATTTGTACCTGTATTATTTCGCC[G/A]
GTGCAATGTTAATTTCCCGCTCCATATTATCACTACCACAAAAATACTCATTGGTGCCAGTTATAAAGGCCTCATAGGTGCCGGTTTTGGGCCCGGCTCC

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	93.70%	2.30%	0.32%	3.72%	NA
All Indica	2759	97.70%	0.10%	0.07%	2.14%	NA
All Japonica	1512	91.90%	6.70%	0.13%	1.26%	NA
Aus	269	60.20%	0.40%	3.72%	35.69%	NA
Indica I	595	98.30%	0.00%	0.17%	1.51%	NA
Indica II	465	97.40%	0.20%	0.00%	2.37%	NA
Indica III	913	96.80%	0.00%	0.00%	3.18%	NA
Indica Intermediate	786	98.30%	0.30%	0.13%	1.27%	NA
Temperate Japonica	767	97.40%	0.30%	0.13%	2.22%	NA
Tropical Japonica	504	80.60%	18.80%	0.20%	0.40%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	1.10%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121334009	C -> T	LOC_Os11g36240.1	upstream_gene_variant ; 1325.0bp to feature; MODIFIER	silent_mutation	Average:57.435; most accessible tissue: Callus, score: 85.173	N	N	N	N
vg1121334009	C -> T	LOC_Os11g36230-LOC_Os11g36240	intergenic_region ; MODIFIER	silent_mutation	Average:57.435; most accessible tissue: Callus, score: 85.173	N	N	N	N
vg1121334009	C -> DEL	N	N	silent_mutation	Average:57.435; most accessible tissue: Callus, score: 85.173	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121334009	5.17E-07	NA	mr1055	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
vg1121334009	NA	3.25E-06	mr1124	Jap_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
vg1121334009	3.48E-07	NA	mr1055_2	Jap_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
vg1121334009	3.09E-06	NA	mr1132_2	Jap_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
vg1121334009	3.82E-06	NA	mr1490_2	Jap_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
vg1121334009	NA	1.50E-07	mr1850_2	Jap_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