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Detailed information for vg1125707575:

Variant ID: vg1125707575 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25707575
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGCTGTTGTGAACTCGGGGTCTGTCCGCAGTTCCAACCTTGGTTGTAATTCTACTCTTAATAAAGAGACCGCTGTTGTTGTGATATTCTATCTTCCTGT[G/T]
GTACCAGCACTGTTTCCTGGGACTGGTACAGGCATACAGGTTAATTTGGATCGCCTTACTCTGGCCGTCGGTTGGGCTAGTTTGGGGTGTGACAGGGATA

Reverse complement sequence

TATCCCTGTCACACCCCAAACTAGCCCAACCGACGGCCAGAGTAAGGCGATCCAAATTAACCTGTATGCCTGTACCAGTCCCAGGAAACAGTGCTGGTAC[C/A]
ACAGGAAGATAGAATATCACAACAACAGCGGTCTCTTTATTAAGAGTAGAATTACAACCAAGGTTGGAACTGCGGACAGACCCCGAGTTCACAACAGCAT

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	33.10%	8.50%	8.68%	49.68%	NA
All Indica	2759	30.20%	12.40%	11.24%	46.25%	NA
All Japonica	1512	40.30%	1.80%	3.37%	54.56%	NA
Aus	269	28.60%	8.20%	12.64%	50.56%	NA
Indica I	595	59.70%	2.00%	10.76%	27.56%	NA
Indica II	465	35.70%	8.80%	6.24%	49.25%	NA
Indica III	913	13.60%	21.40%	13.25%	51.81%	NA
Indica Intermediate	786	23.80%	11.80%	12.21%	52.16%	NA
Temperate Japonica	767	62.10%	0.40%	2.48%	35.07%	NA
Tropical Japonica	504	12.90%	3.00%	5.36%	78.77%	NA
Japonica Intermediate	241	28.20%	3.70%	2.07%	65.98%	NA
VI/Aromatic	96	17.70%	2.10%	11.46%	68.75%	NA
Intermediate	90	34.40%	11.10%	4.44%	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
vg1125707575	G -> T	LOC_Os11g42670.1	upstream_gene_variant ; 3928.0bp to feature; MODIFIER	silent_mutation	Average:22.75; most accessible tissue: Callus, score: 42.964	N	N	N	N
vg1125707575	G -> T	LOC_Os11g42680.1	upstream_gene_variant ; 1305.0bp to feature; MODIFIER	silent_mutation	Average:22.75; most accessible tissue: Callus, score: 42.964	N	N	N	N
vg1125707575	G -> T	LOC_Os11g42690.1	downstream_gene_variant ; 3798.0bp to feature; MODIFIER	silent_mutation	Average:22.75; most accessible tissue: Callus, score: 42.964	N	N	N	N
vg1125707575	G -> T	LOC_Os11g42670-LOC_Os11g42680	intergenic_region ; MODIFIER	silent_mutation	Average:22.75; most accessible tissue: Callus, score: 42.964	N	N	N	N
vg1125707575	G -> DEL	N	N	silent_mutation	Average:22.75; most accessible tissue: Callus, score: 42.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125707575	2.53E-06	NA	mr1407	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
vg1125707575	NA	2.25E-06	mr1408	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
vg1125707575	3.50E-06	3.51E-06	mr1463	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
vg1125707575	NA	1.62E-06	mr1745	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
vg1125707575	NA	5.58E-08	mr1191_2	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
vg1125707575	NA	3.82E-06	mr1662_2	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