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Detailed information for vg1121143927:

Variant ID: vg1121143927 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21143927
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTTGCCAACAAATATGGAAACCATGTCATTGGAAAGCCTCTATCTAGGTTCAAATCAAATAACCGGAGTAATACCGACCCTGCCACCTAACCTCACCTG[G/T]
TTGGAGATCCAAAATAACATGGTATCAAGGATTGTGGCATCAAAAACCTTTGGAGCTCCAAACCTAGGTTATATGGATCTATCCTCCAATAACATCAAAG

Reverse complement sequence

CTTTGATGTTATTGGAGGATAGATCCATATAACCTAGGTTTGGAGCTCCAAAGGTTTTTGATGCCACAATCCTTGATACCATGTTATTTTGGATCTCCAA[C/A]
CAGGTGAGGTTAGGTGGCAGGGTCGGTATTACTCCGGTTATTTGATTTGAACCTAGATAGAGGCTTTCCAATGACATGGTTTCCATATTTGTTGGCAAGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.70%	11.20%	0.11%	0.00%	NA
All Indica	2759	82.70%	17.20%	0.14%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	90.70%	9.30%	0.00%	0.00%	NA
Indica I	595	93.80%	6.10%	0.17%	0.00%	NA
Indica II	465	76.80%	23.00%	0.22%	0.00%	NA
Indica III	913	81.20%	18.80%	0.00%	0.00%	NA
Indica Intermediate	786	79.50%	20.20%	0.25%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg1121143927	G -> T	LOC_Os11g35970.1	upstream_gene_variant ; 1957.0bp to feature; MODIFIER	silent_mutation	Average:44.857; most accessible tissue: Callus, score: 76.022	N	N	N	N
vg1121143927	G -> T	LOC_Os11g35980.1	upstream_gene_variant ; 1833.0bp to feature; MODIFIER	silent_mutation	Average:44.857; most accessible tissue: Callus, score: 76.022	N	N	N	N
vg1121143927	G -> T	LOC_Os11g35970-LOC_Os11g35980	intergenic_region ; MODIFIER	silent_mutation	Average:44.857; most accessible tissue: Callus, score: 76.022	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121143927	1.84E-06	NA	mr1655	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
vg1121143927	1.71E-06	NA	mr1770	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