RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0308557129:

Variant ID: vg0308557129 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8557129
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CAGACTTTTTTATCGATAAACTGTAAAAAGAAAAAACTCAAACTAGTGTTAGTCTGTTAGATATGGGTCCTTCTCAGGTTTCCCTTACCGTCGGTAACCG[C/T]
GGGGTACGATAATGGTTACTAGCGGTAGAGTTTGGGGAATTTTTTTACCAAATTCAAAGTTTTTTTAAAAAAACATGAATGTAGTTCTTGATTTTTAGTG

Reverse complement sequence

CACTAAAAATCAAGAACTACATTCATGTTTTTTTAAAAAAACTTTGAATTTGGTAAAAAAATTCCCCAAACTCTACCGCTAGTAACCATTATCGTACCCC[G/A]
CGGTTACCGACGGTAAGGGAAACCTGAGAAGGACCCATATCTAACAGACTAACACTAGTTTGAGTTTTTTCTTTTTACAGTTTATCGATAAAAAAGTCTG

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	63.60%	36.30%	0.04%	0.00%	NA
All Indica	2759	39.40%	60.50%	0.07%	0.00%	NA
All Japonica	1512	98.70%	1.30%	0.00%	0.00%	NA
Aus	269	97.00%	3.00%	0.00%	0.00%	NA
Indica I	595	2.20%	97.80%	0.00%	0.00%	NA
Indica II	465	26.70%	72.90%	0.43%	0.00%	NA
Indica III	913	66.20%	33.80%	0.00%	0.00%	NA
Indica Intermediate	786	44.10%	55.90%	0.00%	0.00%	NA
Temperate Japonica	767	97.80%	2.20%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	0.00%	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
vg0308557129	C -> T	LOC_Os03g15550.1	upstream_gene_variant ; 1616.0bp to feature; MODIFIER	silent_mutation	Average:44.695; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0308557129	C -> T	LOC_Os03g15540-LOC_Os03g15550	intergenic_region ; MODIFIER	silent_mutation	Average:44.695; most accessible tissue: Zhenshan97 panicle, score: 68.538	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
vg0308557129	NA	1.83E-11	mr1609	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
vg0308557129	NA	5.26E-23	mr1609_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
vg0308557129	NA	4.32E-08	mr1612_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
vg0308557129	NA	7.26E-13	mr1770_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
vg0308557129	NA	9.79E-06	mr1901_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 5 of 5 entries

Previous1Next

Search for Variation information by Variation ID:

Detailed information for vg0308557129:

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