RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1115275633:

Variant ID: vg1115275633 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15275633
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGAAGTTCTCGATGAACCTCCGGTAGTATCCTGCCAAACCCAAAAAACTGCGAATTTGAGTGACTGTCTTGGGTTGCTTCCAATCAGTGACGGCGGTCG[C/T]
TGTTTCGGGGTCCACAGCAACTCCTTTAGCAGATATCACGTGTCCTAAGAATTTGACTTCGGACAACCAAAACTCACACTTGCTAAGTTTGGCATACAAT

Reverse complement sequence

ATTGTATGCCAAACTTAGCAAGTGTGAGTTTTGGTTGTCCGAAGTCAAATTCTTAGGACACGTGATATCTGCTAAAGGAGTTGCTGTGGACCCCGAAACA[G/A]
CGACCGCCGTCACTGATTGGAAGCAACCCAAGACAGTCACTCAAATTCGCAGTTTTTTGGGTTTGGCAGGATACTACCGGAGGTTCATCGAGAACTTCTC

Allele Frequencies:

Search:

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	42.40%	16.80%	16.10%	24.74%	NA
All Indica	2759	40.20%	1.60%	20.62%	37.59%	NA
All Japonica	1512	49.30%	42.70%	5.22%	2.78%	NA
Aus	269	43.10%	0.00%	35.69%	21.19%	NA
Indica I	595	20.20%	2.50%	17.48%	59.83%	NA
Indica II	465	32.30%	1.10%	29.89%	36.77%	NA
Indica III	913	58.80%	0.80%	18.84%	21.58%	NA
Indica Intermediate	786	38.40%	2.20%	19.59%	39.82%	NA
Temperate Japonica	767	82.40%	6.90%	6.78%	3.91%	NA
Tropical Japonica	504	3.60%	91.70%	2.78%	1.98%	NA
Japonica Intermediate	241	39.40%	54.40%	5.39%	0.83%	NA
VI/Aromatic	96	8.30%	84.40%	5.21%	2.08%	NA
Intermediate	90	26.70%	25.60%	13.33%	34.44%	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
vg1115275633	C -> T	LOC_Os11g26670.1	missense_variant ; p.Ala1115Thr; MODERATE	nonsynonymous_codon ; A1115T	Average:6.425; most accessible tissue: Minghui63 root, score: 13.235	benign	0.343	DELETERIOUS	0.00
vg1115275633	C -> DEL	LOC_Os11g26670.1	N	frameshift_variant	Average:6.425; most accessible tissue: Minghui63 root, score: 13.235	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
vg1115275633	NA	5.09E-06	mr1013	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
vg1115275633	NA	1.19E-06	mr1029	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
vg1115275633	NA	1.73E-06	mr1031	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
vg1115275633	NA	1.63E-10	mr1047	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
vg1115275633	NA	6.40E-07	mr1189	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
vg1115275633	NA	5.71E-07	mr1338	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
vg1115275633	NA	3.26E-07	mr1401	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
vg1115275633	NA	1.61E-12	mr1449	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
vg1115275633	7.04E-06	2.31E-07	mr1502	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
vg1115275633	NA	2.02E-06	mr1502	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

Showing 1 to 10 of 52 entries

Previous1 2 3 4 5 6Next

Search for Variation information by Variation ID:

Detailed information for vg1115275633:

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