RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0210660828:

Variant ID: vg0210660828 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10660828
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: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GACTTGTTTGATCAGCTTAAAGATGCCACCGTTTTCTCCAAGATCGATCTTCGATCAAGGTATCACCAGTTGAGGATCAAAGAGGAAGATATACCTAAGA[C/T]
GGCTTTTACCACTCGGTATGGGTTGTTTGAATGTACTGTTATGTCTGTTGGACTTACCAATGCCCCCGCTTTCTTCATGAACTTGATGAATAAGGTGTTT

Reverse complement sequence

AAACACCTTATTCATCAAGTTCATGAAGAAAGCGGGGGCATTGGTAAGTCCAACAGACATAACAGTACATTCAAACAACCCATACCGAGTGGTAAAAGCC[G/A]
TCTTAGGTATATCTTCCTCTTTGATCCTCAACTGGTGATACCTTGATCGAAGATCGATCTTGGAGAAAACGGTGGCATCTTTAAGCTGATCAAACAAGTC

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	93.40%	4.60%	1.97%	0.00%	NA
All Indica	2759	99.30%	0.20%	0.54%	0.00%	NA
All Japonica	1512	81.70%	13.80%	4.50%	0.00%	NA
Aus	269	96.70%	0.40%	2.97%	0.00%	NA
Indica I	595	98.70%	0.00%	1.34%	0.00%	NA
Indica II	465	98.90%	0.20%	0.86%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.30%	0.38%	0.00%	NA
Temperate Japonica	767	66.10%	26.30%	7.56%	0.00%	NA
Tropical Japonica	504	98.60%	0.00%	1.39%	0.00%	NA
Japonica Intermediate	241	95.90%	2.90%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0210660828	C -> T	LOC_Os02g18340.1	missense_variant ; p.Thr772Met; MODERATE	nonsynonymous_codon ; T772M	Average:37.605; most accessible tissue: Minghui63 flag leaf, score: 59.912	probably damaging	2.645	DELETERIOUS	0.00

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210660828	7.96E-07	NA	mr1300	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
vg0210660828	4.67E-09	NA	mr1310	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
vg0210660828	NA	9.83E-08	mr1310	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
vg0210660828	NA	9.11E-10	mr1712	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
vg0210660828	7.71E-10	NA	mr1926	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
vg0210660828	NA	5.72E-08	mr1926	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
vg0210660828	NA	3.06E-09	mr1959	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 7 of 7 entries

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Search for Variation information by Variation ID:

Detailed information for vg0210660828:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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