RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0412260112:

Variant ID: vg0412260112 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12260112
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTCCTTCCTATGTTGTACCACTCTTTTTCGTAAGAACGTTTGTAAACTATGTTTTTTTTCTCAAAAGTCTTCTATGTAAAAAATATACTCCTTGTCTT[G/C]
ATGGGCCCATAAACACCGGTTGACATAGTCAACCACCTCAGTGAAGCTCTGTTGTAAATTAACCTCGTTCACCATGGATGGATCAAGGAACCCAACTTGA

Reverse complement sequence

TCAAGTTGGGTTCCTTGATCCATCCATGGTGAACGAGGTTAATTTACAACAGAGCTTCACTGAGGTGGTTGACTATGTCAACCGGTGTTTATGGGCCCAT[C/G]
AAGACAAGGAGTATATTTTTTACATAGAAGACTTTTGAGAAAAAAAACATAGTTTACAAACGTTCTTACGAAAAAGAGTGGTACAACATAGGAAGGACAT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.50%	27.20%	19.11%	3.15%	NA
All Indica	2759	42.20%	40.10%	14.50%	3.19%	NA
All Japonica	1512	67.10%	0.90%	28.51%	3.44%	NA
Aus	269	50.90%	48.70%	0.37%	0.00%	NA
Indica I	595	48.60%	24.90%	23.70%	2.86%	NA
Indica II	465	41.10%	48.40%	9.46%	1.08%	NA
Indica III	913	43.40%	36.10%	15.12%	5.37%	NA
Indica Intermediate	786	36.80%	51.30%	9.80%	2.16%	NA
Temperate Japonica	767	85.40%	0.40%	13.56%	0.65%	NA
Tropical Japonica	504	43.10%	1.00%	49.01%	6.94%	NA
Japonica Intermediate	241	59.30%	2.50%	33.20%	4.98%	NA
VI/Aromatic	96	30.20%	4.20%	56.25%	9.38%	NA
Intermediate	90	46.70%	34.40%	18.89%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412260112	G -> C	LOC_Os04g21670.1	missense_variant ; p.Gln176Glu; MODERATE	nonsynonymous_codon ; Q176E	Average:32.789; most accessible tissue: Zhenshan97 flower, score: 45.068	benign	0.215	DELETERIOUS	0.02
vg0412260112	G -> DEL	LOC_Os04g21670.1	N	frameshift_variant	Average:32.789; most accessible tissue: Zhenshan97 flower, score: 45.068	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412260112	NA	9.21E-08	mr1062	Ind_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
vg0412260112	NA	3.65E-07	mr1386	Ind_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
vg0412260112	NA	2.01E-07	mr1403	Ind_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
vg0412260112	NA	1.89E-06	mr1414	Ind_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
vg0412260112	NA	7.33E-06	mr1525	Ind_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
vg0412260112	NA	8.43E-09	mr1830	Ind_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
vg0412260112	1.55E-07	1.53E-19	mr1846	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
vg0412260112	7.75E-08	2.35E-15	mr1846	Ind_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
vg0412260112	NA	7.18E-08	mr1317_2	Ind_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
vg0412260112	NA	1.96E-07	mr1608_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

Showing 1 to 10 of 16 entries

Previous1 2Next

Search for Variation information by Variation ID:

Detailed information for vg0412260112:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

RiceVarMap v2.0

Tools

Blast

Design Primer by Variation ID

Design Primer by Region

Haplotype Network Analysis

Varitation Coordinate Convert

Contact