Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1119170327:

Variant ID: vg1119170327 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19170327
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, C: 0.30, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TTATGATGATGCTTGGATCCTCATGTGTTAGTTTTGCTTTTCTCATATGTGTAGTCGGTATTATTCATATTAGAAAGCATATTATTCAGTGTTTACAGTA[T/C]
CTGTTTAGCAGGAAGCACCTTCATTTTGAAATATTTAAATTCAACATTTTGCTGCCCCTATATTTGTTACTTGTTCTTTTCCTTTCTCATGTTGAAGTGT

Reverse complement sequence

ACACTTCAACATGAGAAAGGAAAAGAACAAGTAACAAATATAGGGGCAGCAAAATGTTGAATTTAAATATTTCAAAATGAAGGTGCTTCCTGCTAAACAG[A/G]
TACTGTAAACACTGAATAATATGCTTTCTAATATGAATAATACCGACTACACATATGAGAAAAGCAAAACTAACACATGAGGATCCAAGCATCATCATAA

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	50.00%	49.60%	0.36%	0.00%	NA
All Indica	2759	27.20%	72.20%	0.54%	0.00%	NA
All Japonica	1512	91.60%	8.30%	0.07%	0.00%	NA
Aus	269	40.10%	59.90%	0.00%	0.00%	NA
Indica I	595	58.50%	41.50%	0.00%	0.00%	NA
Indica II	465	9.50%	90.10%	0.43%	0.00%	NA
Indica III	913	16.50%	82.90%	0.55%	0.00%	NA
Indica Intermediate	786	26.50%	72.50%	1.02%	0.00%	NA
Temperate Japonica	767	96.50%	3.50%	0.00%	0.00%	NA
Tropical Japonica	504	87.30%	12.50%	0.20%	0.00%	NA
Japonica Intermediate	241	85.10%	14.90%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	16.70%	1.04%	0.00%	NA
Intermediate	90	45.60%	54.40%	0.00%	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
vg1119170327	T -> C	LOC_Os11g32480.1	upstream_gene_variant ; 2561.0bp to feature; MODIFIER	silent_mutation	Average:49.967; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg1119170327	T -> C	LOC_Os11g32490.1	downstream_gene_variant ; 4822.0bp to feature; MODIFIER	silent_mutation	Average:49.967; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N
vg1119170327	T -> C	LOC_Os11g32470.1	intron_variant ; MODIFIER	silent_mutation	Average:49.967; most accessible tissue: Minghui63 flag leaf, score: 64.867	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119170327	NA	4.22E-06	mr1629	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
vg1119170327	3.56E-07	3.56E-07	mr1655	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
vg1119170327	NA	2.03E-06	mr1712	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
vg1119170327	4.74E-07	4.74E-07	mr1770	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
vg1119170327	NA	2.68E-06	mr1887	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
vg1119170327	3.00E-06	3.00E-06	mr1910	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
vg1119170327	NA	8.40E-10	mr1935	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