RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1125246415:

Variant ID: vg1125246415 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25246415
Reference Allele: C	Alternative Allele: T,G
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: 331. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGCCCGAGGTGCAATGGCGGCTGCTCACATGAAACCATCGTCGGCATTGTCCAAGCAGTGTTCAAGCACCATGCGTACTCTAAGCTGCACAAGGGACA[C/T,G]
CTTGGGATGTTAGTTTAAGCACAAACCAAGGTTTGTAAGGTTCAAGAACATATGCCGACAAATGCTAACCAACTACCAGACATGTTTGTCATCTTGCATT

Reverse complement sequence

AATGCAAGATGACAAACATGTCTGGTAGTTGGTTAGCATTTGTCGGCATATGTTCTTGAACCTTACAAACCTTGGTTTGTGCTTAAACTAACATCCCAAG[G/A,C]
TGTCCCTTGTGCAGCTTAGAGTACGCATGGTGCTTGAACACTGCTTGGACAATGCCGACGATGGTTTCATGTGAGCAGCCGCCATTGCACCTCGGGCCAT

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	96.50%	3.50%	0.00%	0.00%	G: 0.02%
All Indica	2759	95.40%	4.60%	0.00%	0.00%	G: 0.04%
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	84.70%	15.10%	0.00%	0.00%	G: 0.22%
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	93.10%	6.90%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	97.20%	2.80%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg1125246415	C -> T	LOC_Os11g41990.1	intron_variant ; MODIFIER	silent_mutation	Average:67.111; most accessible tissue: Zhenshan97 young leaf, score: 78.938	N	N	N	N
vg1125246415	C -> T	LOC_Os11g41990.2	intron_variant ; MODIFIER	silent_mutation	Average:67.111; most accessible tissue: Zhenshan97 young leaf, score: 78.938	N	N	N	N
vg1125246415	C -> G	LOC_Os11g41990.1	intron_variant ; MODIFIER	silent_mutation	Average:67.111; most accessible tissue: Zhenshan97 young leaf, score: 78.938	N	N	N	N
vg1125246415	C -> G	LOC_Os11g41990.2	intron_variant ; MODIFIER	silent_mutation	Average:67.111; most accessible tissue: Zhenshan97 young leaf, score: 78.938	N	N	N	N

Showing 1 to 4 of 4 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125246415	5.45E-16	5.25E-17	mr1238	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
vg1125246415	1.66E-10	2.67E-11	mr1309	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
vg1125246415	8.79E-07	1.11E-07	mr1484	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
vg1125246415	2.34E-08	1.08E-08	mr1841	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
vg1125246415	2.13E-12	1.40E-13	mr1238_2	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
vg1125246415	5.95E-12	1.26E-13	mr1484_2	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
vg1125246415	9.29E-14	4.18E-14	mr1841_2	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
vg1125246415	3.62E-08	2.67E-09	mr1900_2	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
vg1125246415	2.27E-08	2.27E-08	mr1945_2	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

Showing 1 to 9 of 9 entries

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Search for Variation information by Variation ID:

Detailed information for vg1125246415:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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