Search for Variation information by Variation ID:

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

Detailed information for vg0118565792:

Variant ID: vg0118565792 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 18565792
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

AACTCAAACAGTGGAAGAGTTGTTACAACAGATGCGACGTCGGTACCAAATATACCAGATGCAACGGCAATGTCAGGAGTCGCGTCAATGTCACCAACCG[C/T]
AGGTGCAAGTCCAGATGCCAGCCCAGAACCCGAATCAGAGTCAGAGTCAGGAGTTCCCAATATTGGCACCGAAGACCCCTGTCAAAATGCTGTCCAGATC

Reverse complement sequence

GATCTGGACAGCATTTTGACAGGGGTCTTCGGTGCCAATATTGGGAACTCCTGACTCTGACTCTGATTCGGGTTCTGGGCTGGCATCTGGACTTGCACCT[G/A]
CGGTTGGTGACATTGACGCGACTCCTGACATTGCCGTTGCATCTGGTATATTTGGTACCGACGTCGCATCTGTTGTAACAACTCTTCCACTGTTTGAGTT

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	73.30%	14.30%	2.64%	9.73%	NA
All Indica	2759	74.10%	24.00%	0.29%	1.63%	NA
All Japonica	1512	66.90%	0.10%	6.48%	26.52%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	93.90%	6.10%	0.00%	0.00%	NA
Indica II	465	96.10%	3.40%	0.22%	0.22%	NA
Indica III	913	45.00%	50.80%	0.55%	3.61%	NA
Indica Intermediate	786	79.90%	18.40%	0.25%	1.40%	NA
Temperate Japonica	767	69.60%	0.00%	3.00%	27.38%	NA
Tropical Japonica	504	64.90%	0.00%	12.10%	23.02%	NA
Japonica Intermediate	241	62.20%	0.80%	5.81%	31.12%	NA
VI/Aromatic	96	66.70%	3.10%	16.67%	13.54%	NA
Intermediate	90	85.60%	11.10%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0118565792	C -> T	LOC_Os01g33740.1	missense_variant ; p.Ala898Thr; MODERATE	nonsynonymous_codon ; A898T	Average:21.562; most accessible tissue: Minghui63 root, score: 38.567	unknown	unknown	TOLERATED	0.13
vg0118565792	C -> DEL	LOC_Os01g33740.1	N	frameshift_variant	Average:21.562; most accessible tissue: Minghui63 root, score: 38.567	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0118565792	NA	3.31E-07	mr1076	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
vg0118565792	NA	1.09E-07	mr1082	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
vg0118565792	NA	6.78E-06	mr1083	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
vg0118565792	NA	1.93E-06	mr1411	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
vg0118565792	NA	6.58E-06	mr1560	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
vg0118565792	NA	1.58E-06	mr1082_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
vg0118565792	9.99E-07	9.95E-09	mr1107_2	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
vg0118565792	NA	4.26E-06	mr1226_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
vg0118565792	NA	3.35E-07	mr1227_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