Search for Variation information by Variation ID:

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

Detailed information for vg1217121743:

Variant ID: vg1217121743 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17121743
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TTGATGAAAGTTACTCAAAGCATTCCAAATTTCATGAGCAGCTCAAAAATGCGCAACACGATCATAATCCGAACGAGAAATACCACTCAAAAGAATGTTG[T/C]
GAGCTTTGCAATTTTGTTCAAAAGCAGTTTTTTCAGCAGCAGTATTAATAGCTTCAGGAATCACATAGGGACGAGAAACTTTTCTCCAAATATCATAAAC

Reverse complement sequence

GTTTATGATATTTGGAGAAAAGTTTCTCGTCCCTATGTGATTCCTGAAGCTATTAATACTGCTGCTGAAAAAACTGCTTTTGAACAAAATTGCAAAGCTC[A/G]
CAACATTCTTTTGAGTGGTATTTCTCGTTCGGATTATGATCGTGTTGCGCATTTTTGAGCTGCTCATGAAATTTGGAATGCTTTGAGTAACTTTCATCAA

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	90.30%	6.70%	0.11%	2.84%	NA
All Indica	2759	97.20%	1.30%	0.07%	1.45%	NA
All Japonica	1512	93.70%	0.20%	0.20%	5.95%	NA
Aus	269	18.60%	81.00%	0.00%	0.37%	NA
Indica I	595	97.10%	0.00%	0.17%	2.69%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	96.70%	1.30%	0.00%	1.97%	NA
Indica Intermediate	786	96.30%	2.80%	0.13%	0.76%	NA
Temperate Japonica	767	97.70%	0.00%	0.00%	2.35%	NA
Tropical Japonica	504	90.10%	0.00%	0.60%	9.33%	NA
Japonica Intermediate	241	88.40%	1.20%	0.00%	10.37%	NA
VI/Aromatic	96	41.70%	58.30%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217121743	T -> C	LOC_Os12g28950.1	missense_variant ; p.His46Arg; MODERATE	nonsynonymous_codon ; H46R	Average:23.195; most accessible tissue: Minghui63 flag leaf, score: 32.882	unknown	unknown	TOLERATED	1.00
vg1217121743	T -> DEL	LOC_Os12g28950.1	N	frameshift_variant	Average:23.195; most accessible tissue: Minghui63 flag leaf, score: 32.882	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217121743	NA	8.37E-10	mr1570	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
vg1217121743	2.70E-06	NA	mr1741	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
vg1217121743	NA	7.96E-07	mr1803	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
vg1217121743	NA	9.78E-06	mr1158_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
vg1217121743	NA	1.32E-10	mr1166_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
vg1217121743	NA	1.74E-06	mr1369_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
vg1217121743	NA	3.91E-07	mr1453_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
vg1217121743	NA	3.59E-06	mr1522_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
vg1217121743	NA	1.73E-07	mr1567_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
vg1217121743	NA	2.57E-08	mr1762_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
vg1217121743	NA	1.58E-07	mr1765_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
vg1217121743	NA	3.61E-06	mr1929_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
vg1217121743	NA	3.58E-10	mr1942_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