Search for Variation information by Variation ID:

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

Detailed information for vg0103977465:

Variant ID: vg0103977465 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3977465
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTTGGTCAGTGCATCAATTTCTGAATTTTGTCATACTACTGTAGTTTGCAATCTTTGCTCTTTCTGCATTAGGACCAGATAGTTTGTTCCTCAGACTG[C/T]
CATTGTTCTTGGGCCAATAGGATGGTTACAAATTGATCATTTGATTAGCTTGATTAGTACTACACTTACATTTGTGCATGTGCGAGACACGAGTATTATT

Reverse complement sequence

AATAATACTCGTGTCTCGCACATGCACAAATGTAAGTGTAGTACTAATCAAGCTAATCAAATGATCAATTTGTAACCATCCTATTGGCCCAAGAACAATG[G/A]
CAGTCTGAGGAACAAACTATCTGGTCCTAATGCAGAAAGAGCAAAGATTGCAAACTACAGTAGTATGACAAAATTCAGAAATTGATGCACTGACCAACAG

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	93.40%	6.60%	0.00%	0.00%	NA
All Indica	2759	94.20%	5.80%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	56.10%	43.90%	0.00%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	94.50%	5.50%	0.00%	0.00%	NA
Indica Intermediate	786	91.10%	8.90%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	70.80%	29.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0103977465	C -> T	LOC_Os01g08190.1	intron_variant ; MODIFIER	silent_mutation	Average:54.713; most accessible tissue: Callus, score: 88.431	N	N	N	N
vg0103977465	C -> T	LOC_Os01g08190.2	intron_variant ; MODIFIER	silent_mutation	Average:54.713; most accessible tissue: Callus, score: 88.431	N	N	N	N
vg0103977465	C -> T	LOC_Os01g08190.5	intron_variant ; MODIFIER	silent_mutation	Average:54.713; most accessible tissue: Callus, score: 88.431	N	N	N	N
vg0103977465	C -> T	LOC_Os01g08190.3	intron_variant ; MODIFIER	silent_mutation	Average:54.713; most accessible tissue: Callus, score: 88.431	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103977465	NA	3.37E-06	mr1028	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
vg0103977465	NA	5.07E-06	mr1262	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
vg0103977465	NA	7.52E-06	mr1331	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
vg0103977465	NA	1.71E-07	mr1365	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
vg0103977465	3.65E-06	3.64E-06	mr1421	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
vg0103977465	NA	5.06E-06	mr1424	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
vg0103977465	NA	6.67E-08	mr1574	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
vg0103977465	NA	9.92E-10	mr1866	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