Search for Variation information by Variation ID:

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

Detailed information for vg1119170143:

Variant ID: vg1119170143 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19170143
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GATGAACTTACTCCCTCTGATCCCCCCCCCCCAAAAAAAAAGAAAGAAAAAAACCAACCTAGTATGGGATGGGGCATAATCTAGTACAACGATGTAGACA[C/T]
GCTCCTGTCCAGATTCATTATGTTCTATCTCGTACTAGGTTGGGTTTTTTTGGGACGGAGGGAGTACAGGTTTATACCCGAAGTTATGATGATGCTTGGA

Reverse complement sequence

TCCAAGCATCATCATAACTTCGGGTATAAACCTGTACTCCCTCCGTCCCAAAAAAACCCAACCTAGTACGAGATAGAACATAATGAATCTGGACAGGAGC[G/A]
TGTCTACATCGTTGTACTAGATTATGCCCCATCCCATACTAGGTTGGTTTTTTTCTTTCTTTTTTTTTGGGGGGGGGGGATCAGAGGGAGTAAGTTCATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	49.50%	0.19%	0.25%	NA
All Indica	2759	27.10%	72.20%	0.29%	0.43%	NA
All Japonica	1512	91.70%	8.30%	0.00%	0.00%	NA
Aus	269	40.90%	59.10%	0.00%	0.00%	NA
Indica I	595	58.20%	41.30%	0.34%	0.17%	NA
Indica II	465	9.50%	90.10%	0.22%	0.22%	NA
Indica III	913	16.50%	82.70%	0.22%	0.55%	NA
Indica Intermediate	786	26.30%	72.60%	0.38%	0.64%	NA
Temperate Japonica	767	96.50%	3.50%	0.00%	0.00%	NA
Tropical Japonica	504	87.50%	12.50%	0.00%	0.00%	NA
Japonica Intermediate	241	85.50%	14.50%	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
vg1119170143	C -> T	LOC_Os11g32480.1	upstream_gene_variant ; 2745.0bp to feature; MODIFIER	silent_mutation	Average:56.993; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg1119170143	C -> T	LOC_Os11g32470.1	intron_variant ; MODIFIER	silent_mutation	Average:56.993; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg1119170143	C -> DEL	N	N	silent_mutation	Average:56.993; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119170143	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
vg1119170143	NA	2.90E-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
vg1119170143	1.98E-07	1.98E-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
vg1119170143	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
vg1119170143	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
vg1119170143	3.58E-06	NA	mr1748_2	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