RiceVarMap2

Detailed information for vg0403668263:

Variant ID: vg0403668263 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 3668263

Reference Allele: A

Alternative Allele: G

Primary Allele: G

Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.14, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTATTATTCCTTTTAGAAAATGATTTTTATTTTGGGATGAATTTATCAGGACGTGACAAAGATGTTCCTTCCCCTTCTCAACAAAACCTTCTGGCTGA[A/G]
AGACATATACTTCTTCCTCAAGATCACCATTAAGGAATGCCGACTTGACGTCAAGGTGATGCACCTGCCACCTTCGATCAGCTGCAACTGCAAGTATAGC

Reverse complement sequence

GCTATACTTGCAGTTGCAGCTGATCGAAGGTGGCAGGTGCATCACCTTGACGTCAAGTCGGCATTCCTTAATGGTGATCTTGAGGAAGAAGTATATGTCT[T/C]
TCAGCCAGAAGGTTTTGTTGAGAAGGGGAAGGAACATCTTTGTCACGTCCTGATAAATTCATCCCAAAATAAAAATCATTTTCTAAAAGGAATAATAGAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.30%	10.10%	1.46%	22.22%	NA
All Indica	2759	88.10%	4.00%	2.03%	5.87%	NA
All Japonica	1512	19.80%	23.90%	0.46%	55.75%	NA
Aus	269	92.20%	0.00%	1.49%	6.32%	NA
Indica I	595	97.00%	1.20%	0.50%	1.34%	NA
Indica II	465	83.40%	6.20%	0.43%	9.89%	NA
Indica III	913	88.40%	4.70%	4.05%	2.85%	NA
Indica Intermediate	786	84.00%	3.80%	1.78%	10.43%	NA
Temperate Japonica	767	3.10%	40.30%	0.65%	55.93%	NA
Tropical Japonica	504	31.00%	4.40%	0.40%	64.29%	NA
Japonica Intermediate	241	49.80%	12.90%	0.00%	37.34%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	74.40%	5.60%	2.22%	17.78%	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
vg0403668263	A -> DEL	LOC_Os04g06960.1	N	frameshift_variant	Average:25.219; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0403668263	A -> G	LOC_Os04g06960.1	missense_variant ; p.Phe849Ser; MODERATE	nonsynonymous_codon ; F849S	Average:25.219; most accessible tissue: Minghui63 panicle, score: 38.588	possibly damaging	-1.775	TOLERATED	0.64

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403668263	1.96E-06	NA	mr1588_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

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/

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Detailed information for vg0403668263:

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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