Search for Variation information by Variation ID:

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

Detailed information for vg1106643219:

Variant ID: vg1106643219 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6643219
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGAGGACCTAGTTAGCTAGTCGGCAACTGCAAAAATATAATTCCAGTCTCCTTATTCTACTCACTAATGACAGCTTAGAGAAAGCTAACAAACTGATTT[C/T]
TTATGTTTTCATCCAACTAAAACGGCCGGAGACCTCCAAGTCGTCTTAGTATAAAAATCTCTCAAGTCAAGTTTCCTCGATTTCTTGGTCGTCGTCTTCG

Reverse complement sequence

CGAAGACGACGACCAAGAAATCGAGGAAACTTGACTTGAGAGATTTTTATACTAAGACGACTTGGAGGTCTCCGGCCGTTTTAGTTGGATGAAAACATAA[G/A]
AAATCAGTTTGTTAGCTTTCTCTAAGCTGTCATTAGTGAGTAGAATAAGGAGACTGGAATTATATTTTTGCAGTTGCCGACTAGCTAACTAGGTCCTCAA

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	53.90%	10.20%	0.40%	35.46%	NA
All Indica	2759	26.20%	16.50%	0.58%	56.76%	NA
All Japonica	1512	94.00%	0.50%	0.13%	5.42%	NA
Aus	269	95.20%	4.10%	0.37%	0.37%	NA
Indica I	595	33.80%	0.20%	0.34%	65.71%	NA
Indica II	465	7.50%	17.60%	0.65%	74.19%	NA
Indica III	913	30.60%	27.40%	0.33%	41.73%	NA
Indica Intermediate	786	26.30%	15.50%	1.02%	57.12%	NA
Temperate Japonica	767	96.00%	0.40%	0.26%	3.39%	NA
Tropical Japonica	504	91.90%	0.40%	0.00%	7.74%	NA
Japonica Intermediate	241	92.10%	0.80%	0.00%	7.05%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	58.90%	11.10%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106643219	C -> T	LOC_Os11g11960.1	upstream_gene_variant ; 2297.0bp to feature; MODIFIER	silent_mutation	Average:24.93; most accessible tissue: Callus, score: 91.749	N	N	N	N
vg1106643219	C -> T	LOC_Os11g11970.1	upstream_gene_variant ; 3214.0bp to feature; MODIFIER	silent_mutation	Average:24.93; most accessible tissue: Callus, score: 91.749	N	N	N	N
vg1106643219	C -> T	LOC_Os11g11960-LOC_Os11g11970	intergenic_region ; MODIFIER	silent_mutation	Average:24.93; most accessible tissue: Callus, score: 91.749	N	N	N	N
vg1106643219	C -> DEL	N	N	silent_mutation	Average:24.93; most accessible tissue: Callus, score: 91.749	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106643219	2.80E-07	2.80E-07	mr1900	Ind_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