RiceVarMap2

Detailed information for vg0227603617:

Variant ID: vg0227603617 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 27603617

Reference Allele: G

Alternative Allele: A

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGCAATGCAAGCTATTCTTTCTAACAGAAAGATAGATGGGCATTGCCTTTTTAAAACCTAACTAAGCTTCAAATGTGGAAAAAATGCTTGCTCCAAAT[G/A]
CGTCTGAAAAATCCTAGTAACAATGAGGTGATAAAATGGAGAAGGAAATTATGTGTCTGAATTGAGCAAGGAGTGATAACTTGGGAACCAAAAGTACTAC

Reverse complement sequence

GTAGTACTTTTGGTTCCCAAGTTATCACTCCTTGCTCAATTCAGACACATAATTTCCTTCTCCATTTTATCACCTCATTGTTACTAGGATTTTTCAGACG[C/T]
ATTTGGAGCAAGCATTTTTTCCACATTTGAAGCTTAGTTAGGTTTTAAAAAGGCAATGCCCATCTATCTTTCTGTTAGAAAGAATAGCTTGCATTGCAAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.60%	39.30%	0.08%	0.02%	NA
All Indica	2759	96.60%	3.30%	0.11%	0.00%	NA
All Japonica	1512	0.70%	99.30%	0.00%	0.00%	NA
Aus	269	56.10%	43.90%	0.00%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	98.70%	1.10%	0.22%	0.00%	NA
Indica Intermediate	786	93.50%	6.40%	0.13%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	40.00%	57.80%	1.11%	1.11%	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
vg0227603617	G -> A	LOC_Os02g45390.1	intron_variant ; MODIFIER	silent_mutation	Average:33.661; most accessible tissue: Callus, score: 47.032	N	N	N	N
vg0227603617	G -> DEL	N	N	silent_mutation	Average:33.661; most accessible tissue: Callus, score: 47.032	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
vg0227603617	NA	2.38E-72	mr1629	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 vg0227603617:

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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