RiceVarMap2

Detailed information for vg0223952985:

Variant ID: vg0223952985 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 23952985

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: 80. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAAGTATTTCTTGCTTTACCACTGTGCAGGTAGCTCGCCATGCTCGTAGCTTTGTTTGCGGCGTTAGTACTCCTCTGCTACTCAGCCGGCAACATCCA[C/T]
TGCGTCGTGGCGGTCCATGGAAACGACTCCGACATGCTCGCGCTGCTCGAGTTCAAGGATGCCATCGGCGACGATCCGGCGGGCGTCCTGAGCTCCTGGA

Reverse complement sequence

TCCAGGAGCTCAGGACGCCCGCCGGATCGTCGCCGATGGCATCCTTGAACTCGAGCAGCGCGAGCATGTCGGAGTCGTTTCCATGGACCGCCACGACGCA[G/A]
TGGATGTTGCCGGCTGAGTAGCAGAGGAGTACTAACGCCGCAAACAAAGCTACGAGCATGGCGAGCTACCTGCACAGTGGTAAAGCAAGAAATACTTAGT

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	71.10%	12.20%	0.49%	16.23%	NA
All Indica	2759	55.60%	19.40%	0.76%	24.28%	NA
All Japonica	1512	96.10%	2.30%	0.00%	1.59%	NA
Aus	269	80.70%	0.00%	0.74%	18.59%	NA
Indica I	595	69.40%	15.30%	0.67%	14.62%	NA
Indica II	465	64.10%	25.40%	0.43%	10.11%	NA
Indica III	913	44.20%	16.20%	0.99%	38.55%	NA
Indica Intermediate	786	53.30%	22.50%	0.76%	23.41%	NA
Temperate Japonica	767	98.00%	1.00%	0.00%	0.91%	NA
Tropical Japonica	504	92.50%	5.00%	0.00%	2.58%	NA
Japonica Intermediate	241	97.50%	0.80%	0.00%	1.66%	NA
VI/Aromatic	96	78.10%	3.10%	0.00%	18.75%	NA
Intermediate	90	90.00%	4.40%	0.00%	5.56%	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
vg0223952985	C -> T	LOC_Os02g39660.1	synonymous_variant ; p.His20His; LOW	synonymous_codon	Average:79.102; most accessible tissue: Callus, score: 91.84	N	N	N	N
vg0223952985	C -> DEL	LOC_Os02g39660.1	N	frameshift_variant	Average:79.102; most accessible tissue: Callus, score: 91.84	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223952985	NA	7.92E-06	mr1236	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

Contact

Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China

Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/

Search for Variation information by Variation ID:

Detailed information for vg0223952985:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

RiceVarMap v2.0

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