Search for Variation information by Variation ID:

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

Detailed information for vg0221017633:

Variant ID: vg0221017633 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21017633
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTAAAAAAAACTTAGGTGTTAAGTTTTCTTTGGCTTTTACCAATATGTGATCAGCAATCACTATTTCTGCATTTGGTCATTTTCTACTTTTCTTCAAA[C/T]
GACCAATTTCATAACATCTCCTCTATTACTTTCAGACCAAGACCAGAAAGTCATATGTGTCATAGCTTTCTTTCTTTCTTCTTGTTTTTTTTAAAGGAAT

Reverse complement sequence

ATTCCTTTAAAAAAAACAAGAAGAAAGAAAGAAAGCTATGACACATATGACTTTCTGGTCTTGGTCTGAAAGTAATAGAGGAGATGTTATGAAATTGGTC[G/A]
TTTGAAGAAAAGTAGAAAATGACCAAATGCAGAAATAGTGATTGCTGATCACATATTGGTAAAAGCCAAAGAAAACTTAACACCTAAGTTTTTTTTAAAA

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	56.80%	42.70%	0.02%	0.49%	NA
All Indica	2759	38.30%	60.90%	0.00%	0.76%	NA
All Japonica	1512	94.00%	6.00%	0.00%	0.00%	NA
Aus	269	21.60%	77.70%	0.00%	0.74%	NA
Indica I	595	21.20%	78.20%	0.00%	0.67%	NA
Indica II	465	35.50%	63.90%	0.00%	0.65%	NA
Indica III	913	56.80%	42.30%	0.00%	0.88%	NA
Indica Intermediate	786	31.40%	67.80%	0.00%	0.76%	NA
Temperate Japonica	767	93.20%	6.80%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	63.30%	36.70%	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
vg0221017633	C -> T	LOC_Os02g35020.1	intron_variant ; MODIFIER	silent_mutation	Average:62.615; most accessible tissue: Zhenshan97 root, score: 88.318	N	N	N	N
vg0221017633	C -> DEL	N	N	silent_mutation	Average:62.615; most accessible tissue: Zhenshan97 root, score: 88.318	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221017633	4.13E-06	8.75E-06	mr1069	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
vg0221017633	4.34E-06	4.34E-06	mr1099	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
vg0221017633	5.56E-07	3.96E-07	mr1101	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
vg0221017633	NA	4.96E-13	mr1149	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
vg0221017633	2.25E-06	3.43E-06	mr1150	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
vg0221017633	NA	9.89E-08	mr1162	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
vg0221017633	NA	2.29E-14	mr1441	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
vg0221017633	NA	1.80E-07	mr1510	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
vg0221017633	NA	3.22E-06	mr1748	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
vg0221017633	3.52E-07	1.77E-08	mr1098_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
vg0221017633	9.43E-06	5.86E-06	mr1099_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
vg0221017633	8.82E-07	2.36E-07	mr1150_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
vg0221017633	NA	4.54E-09	mr1222_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
vg0221017633	8.14E-06	9.80E-06	mr1247_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