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Detailed information for vg1113572172:

Variant ID: vg1113572172 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13572172
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.03, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAAATCATCGTAGCTCCGATTTGAGTGGTTCAAGTTGCTAAATTTTTCTAAAATCAAGATCTACATGTTAAAAATATCCACATGTACTGTTTATGCTT[G/T]
TTTTTGTACTGTTTTGTTGATCTTGTTCTTTTGCTTTAGTTTCCAACGTTCCTGAGGAGAGCGTTTTCGTTTAGGAAGGTTCAGAAGTGTTTGCGGAAGC

Reverse complement sequence

GCTTCCGCAAACACTTCTGAACCTTCCTAAACGAAAACGCTCTCCTCAGGAACGTTGGAAACTAAAGCAAAAGAACAAGATCAACAAAACAGTACAAAAA[C/A]
AAGCATAAACAGTACATGTGGATATTTTTAACATGTAGATCTTGATTTTAGAAAAATTTAGCAACTTGAACCACTCAAATCGGAGCTACGATGATTTAGT

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	61.30%	16.90%	11.21%	10.50%	NA
All Indica	2759	38.40%	26.10%	18.01%	17.43%	NA
All Japonica	1512	95.60%	1.90%	1.92%	0.66%	NA
Aus	269	87.70%	12.30%	0.00%	0.00%	NA
Indica I	595	17.50%	29.10%	29.92%	23.53%	NA
Indica II	465	61.50%	4.70%	17.85%	15.91%	NA
Indica III	913	33.80%	38.80%	11.83%	15.55%	NA
Indica Intermediate	786	45.90%	21.90%	16.28%	15.90%	NA
Temperate Japonica	767	96.70%	2.20%	0.65%	0.39%	NA
Tropical Japonica	504	92.70%	1.60%	4.56%	1.19%	NA
Japonica Intermediate	241	97.90%	1.20%	0.41%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	18.90%	4.44%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1113572172	G -> T	LOC_Os11g23950.1	downstream_gene_variant ; 4063.0bp to feature; MODIFIER	silent_mutation	Average:33.407; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1113572172	G -> T	LOC_Os11g23950-LOC_Os11g23970	intergenic_region ; MODIFIER	silent_mutation	Average:33.407; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1113572172	G -> DEL	N	N	silent_mutation	Average:33.407; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113572172	NA	2.11E-06	mr1550	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
vg1113572172	1.88E-06	1.20E-14	mr1739	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
vg1113572172	NA	1.65E-10	mr1739	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
vg1113572172	NA	9.29E-06	mr1759	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
vg1113572172	NA	1.09E-06	mr1839	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
vg1113572172	NA	6.56E-06	mr1909	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
vg1113572172	NA	8.34E-06	mr1959	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
vg1113572172	NA	2.24E-06	mr1378_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
vg1113572172	NA	1.06E-10	mr1739_2	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