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Detailed information for vg1126389757:

Variant ID: vg1126389757 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26389757
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.21, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TACATCGAGTGGTTATATATATATATATATATATATATATATATAATATTGAGAACATTCTCGATCTCTACGTAATTATGATATACAGTAAAAAAACTAA[T/C]
ACATTTTCTCAAGACGGCTGAAAAAAAGTTCATGAAAAACCCATGAACACCCTCTCCAAACACAAACATGCCAAGGACACCAACCTTGCATACTCAGCTT

Reverse complement sequence

AAGCTGAGTATGCAAGGTTGGTGTCCTTGGCATGTTTGTGTTTGGAGAGGGTGTTCATGGGTTTTTCATGAACTTTTTTTCAGCCGTCTTGAGAAAATGT[A/G]
TTAGTTTTTTTACTGTATATCATAATTACGTAGAGATCGAGAATGTTCTCAATATTATATATATATATATATATATATATATATATAACCACTCGATGTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.40%	29.40%	4.80%	12.36%	NA
All Indica	2759	46.10%	39.30%	3.70%	10.87%	NA
All Japonica	1512	72.30%	8.30%	4.56%	14.88%	NA
Aus	269	1.90%	58.00%	20.07%	20.07%	NA
Indica I	595	51.80%	36.30%	4.20%	7.73%	NA
Indica II	465	39.80%	40.40%	4.09%	15.70%	NA
Indica III	913	44.60%	42.90%	1.97%	10.51%	NA
Indica Intermediate	786	47.30%	36.80%	5.09%	10.81%	NA
Temperate Japonica	767	71.40%	5.30%	6.91%	16.30%	NA
Tropical Japonica	504	73.80%	12.30%	1.79%	12.10%	NA
Japonica Intermediate	241	71.80%	9.10%	2.90%	16.18%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	70.00%	22.20%	2.22%	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
vg1126389757	T -> DEL	N	N	silent_mutation	Average:38.53; most accessible tissue: Callus, score: 70.71	N	N	N	N
vg1126389757	T -> C	LOC_Os11g43710.1	downstream_gene_variant ; 3929.0bp to feature; MODIFIER	silent_mutation	Average:38.53; most accessible tissue: Callus, score: 70.71	N	N	N	N
vg1126389757	T -> C	LOC_Os11g43700-LOC_Os11g43710	intergenic_region ; MODIFIER	silent_mutation	Average:38.53; most accessible tissue: Callus, score: 70.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126389757	2.22E-06	2.22E-06	mr1336	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
vg1126389757	NA	3.16E-08	mr1644	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
vg1126389757	6.30E-06	6.30E-06	mr1701	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
vg1126389757	NA	3.46E-07	mr1829	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
vg1126389757	NA	7.60E-13	mr1902	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
vg1126389757	NA	9.73E-10	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
vg1126389757	NA	8.52E-06	mr1875_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
vg1126389757	NA	3.23E-06	mr1908_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