RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1104366840:

Variant ID: vg1104366840 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4366840
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACGCCACCACTGCGCCCTCTCTTTGCAAGCAGGCGTCGCTGCCGCCTCCCTTCACGCATCACCGTCTCCTCCCTCCCCGTGCTGCCGCCGCCGCTGGTT[G/A]
CGCTGCAAGAGAGGCCAGAGAAGACGAGAAGGGAGGTCGGGAGATGAGTGAGAGGATAGTGTTGAAGATTTGAAGTGAAGTGTATTGAGGATCAGTTTGA

Reverse complement sequence

TCAAACTGATCCTCAATACACTTCACTTCAAATCTTCAACACTATCCTCTCACTCATCTCCCGACCTCCCTTCTCGTCTTCTCTGGCCTCTCTTGCAGCG[C/T]
AACCAGCGGCGGCGGCAGCACGGGGAGGGAGGAGACGGTGATGCGTGAAGGGAGGCGGCAGCGACGCCTGCTTGCAAAGAGAGGGCGCAGTGGTGGCGTC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.20%	9.60%	0.06%	0.17%	NA
All Indica	2759	99.60%	0.30%	0.00%	0.07%	NA
All Japonica	1512	73.50%	26.10%	0.13%	0.26%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	0.90%	0.00%	0.25%	NA
Temperate Japonica	767	97.10%	2.70%	0.13%	0.00%	NA
Tropical Japonica	504	42.50%	56.70%	0.20%	0.60%	NA
Japonica Intermediate	241	63.50%	36.10%	0.00%	0.41%	NA
VI/Aromatic	96	57.30%	41.70%	1.04%	0.00%	NA
Intermediate	90	86.70%	11.10%	0.00%	2.22%	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
vg1104366840	G -> A	LOC_Os11g08285-LOC_Os11g08290	intergenic_region ; MODIFIER	silent_mutation	Average:59.928; most accessible tissue: Zhenshan97 young leaf, score: 76.44	N	N	N	N
vg1104366840	G -> DEL	N	N	silent_mutation	Average:59.928; most accessible tissue: Zhenshan97 young leaf, score: 76.44	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
vg1104366840	3.48E-06	NA	mr1017	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
vg1104366840	3.94E-07	NA	mr1023	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
vg1104366840	2.69E-06	NA	mr1079	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
vg1104366840	NA	7.70E-06	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
vg1104366840	NA	3.03E-07	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
vg1104366840	5.67E-06	NA	mr1107	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
vg1104366840	2.13E-09	NA	mr1132	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
vg1104366840	8.33E-06	2.92E-10	mr1132	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
vg1104366840	2.08E-06	NA	mr1142	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
vg1104366840	8.41E-06	NA	mr1178	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 25 entries

Previous1 2 3Next

Search for Variation information by Variation ID:

Detailed information for vg1104366840:

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