Search for Variation information by Variation ID:

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

Detailed information for vg0123776512:

Variant ID: vg0123776512 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23776512
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.72, C: 0.28, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTCGAGGAATCTCTTCCAAACATATACTGCACTAGTTCTCAACGAGGGTTGCATTGCATTGCGTAGCGTGGACTATCACTAACACACAATGGCTAGAA[T/C]
GGCTAGAACTCCAGTTCATCCACGATCGTCCTCGATTGTAGCTGCATTCACTTACCTTTTGCTAGTCCTCTTCCGAGACGCCATCACCACCGCAGCTGCA

Reverse complement sequence

TGCAGCTGCGGTGGTGATGGCGTCTCGGAAGAGGACTAGCAAAAGGTAAGTGAATGCAGCTACAATCGAGGACGATCGTGGATGAACTGGAGTTCTAGCC[A/G]
TTCTAGCCATTGTGTGTTAGTGATAGTCCACGCTACGCAATGCAATGCAACCCTCGTTGAGAACTAGTGCAGTATATGTTTGGAAGAGATTCCTCGAACA

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	25.60%	18.10%	0.13%	56.14%	NA
All Indica	2759	2.40%	7.60%	0.14%	89.85%	NA
All Japonica	1512	73.10%	19.00%	0.00%	7.87%	NA
Aus	269	0.40%	91.80%	0.00%	7.81%	NA
Indica I	595	2.50%	0.50%	0.00%	96.97%	NA
Indica II	465	2.40%	3.70%	0.22%	93.76%	NA
Indica III	913	0.40%	10.80%	0.00%	88.72%	NA
Indica Intermediate	786	4.60%	11.60%	0.38%	83.46%	NA
Temperate Japonica	767	98.60%	0.90%	0.00%	0.52%	NA
Tropical Japonica	504	40.50%	38.70%	0.00%	20.83%	NA
Japonica Intermediate	241	60.20%	35.70%	0.00%	4.15%	NA
VI/Aromatic	96	6.20%	92.70%	0.00%	1.04%	NA
Intermediate	90	35.60%	25.60%	2.22%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0123776512	T -> DEL	LOC_Os01g41930.1	N	frameshift_variant	Average:61.698; most accessible tissue: Minghui63 root, score: 85.031	N	N	N	N
vg0123776512	T -> C	LOC_Os01g41930.1	missense_variant ; p.Met4Thr; MODERATE	nonsynonymous_codon ; M4T	Average:61.698; most accessible tissue: Minghui63 root, score: 85.031	unknown	unknown	TOLERATED	0.56

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123776512	NA	6.08E-17	mr1484	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
vg0123776512	NA	1.65E-06	mr1815	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
vg0123776512	NA	2.91E-06	mr1925	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
vg0123776512	NA	1.21E-11	mr1945	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
vg0123776512	NA	1.88E-15	mr1013_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
vg0123776512	NA	5.42E-06	mr1268_2	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
vg0123776512	NA	1.73E-07	mr1808_2	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
vg0123776512	NA	5.67E-06	mr1870_2	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