Search for Variation information by Variation ID:

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

Detailed information for vg0719816046:

Variant ID: vg0719816046 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19816046
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CGATTCGGATTATGCCTGGTGTAAGGTTGATAGAAAAAGCACAACCGGGACTTGCCAATTTCTTGGGCGGTCCCTTGTTTCTTGGTCCTCCAAGAAGCAA[A/C]
ATTCCATTGCATTATCCACCGCCAAAGCCGAATATGTCGCCGCCGGTTCTTGTTGTGCCCAACTCCTTTGGATGAAACAAACTCTAAAAGACTTTGGCTA

Reverse complement sequence

TAGCCAAAGTCTTTTAGAGTTTGTTTCATCCAAAGGAGTTGGGCACAACAAGAACCGGCGGCGACATATTCGGCTTTGGCGGTGGATAATGCAATGGAAT[T/G]
TTGCTTCTTGGAGGACCAAGAAACAAGGGACCGCCCAAGAAATTGGCAAGTCCCGGTTGTGCTTTTTCTATCAACCTTACACCAGGCATAATCCGAATCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.90%	20.00%	5.97%	42.15%	NA
All Indica	2759	16.60%	8.10%	6.31%	68.94%	NA
All Japonica	1512	66.20%	24.70%	6.81%	2.25%	NA
Aus	269	5.90%	84.00%	0.37%	9.67%	NA
Indica I	595	14.50%	0.30%	4.37%	80.84%	NA
Indica II	465	9.50%	3.70%	5.59%	81.29%	NA
Indica III	913	18.70%	15.60%	8.43%	57.28%	NA
Indica Intermediate	786	20.10%	8.00%	5.73%	66.16%	NA
Temperate Japonica	767	96.30%	2.50%	0.00%	1.17%	NA
Tropical Japonica	504	17.90%	57.50%	19.84%	4.76%	NA
Japonica Intermediate	241	71.40%	27.00%	1.24%	0.41%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	31.10%	31.10%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719816046	A -> DEL	LOC_Os07g33190.1	N	frameshift_variant	Average:6.392; most accessible tissue: Callus, score: 16.503	N	N	N	N
vg0719816046	A -> C	LOC_Os07g33190.1	missense_variant ; p.Asn318His; MODERATE	nonsynonymous_codon	Average:6.392; most accessible tissue: Callus, score: 16.503	probably damaging	2.554	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719816046	NA	9.73E-06	mr1236	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
vg0719816046	NA	2.07E-09	mr1248	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
vg0719816046	NA	2.97E-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
vg0719816046	NA	2.71E-06	mr1295	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
vg0719816046	NA	2.87E-06	mr1443	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
vg0719816046	NA	4.09E-07	mr1733	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
vg0719816046	NA	2.21E-13	mr1769	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
vg0719816046	NA	2.71E-06	mr1780	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
vg0719816046	NA	1.21E-07	mr1942	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
vg0719816046	NA	4.38E-10	mr1047_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
vg0719816046	NA	3.93E-12	mr1189_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
vg0719816046	NA	8.59E-07	mr1295_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
vg0719816046	NA	9.65E-07	mr1346_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
vg0719816046	NA	1.13E-09	mr1364_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
vg0719816046	NA	1.05E-07	mr1563_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
vg0719816046	NA	5.08E-08	mr1642_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
vg0719816046	2.53E-06	NA	mr1923_2	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