RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0816260638:

Variant ID: vg0816260638 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16260638
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTTGCGAGTGATGGAAGTGACATATCTAACATATTGTTCTTCTTATTTTGGGGACTGTTCTGAACTTCCTGTAAAACATCAGTGATAGGAGGCACAA[G/A]
CATAGCTTGTTGCCCCGTTGGGTTCTCCAAAATTTTGCGCTCAACGTTGCAAGCAAGCATGAACAATTGGCCTATATGATTATATGTCACATTATCAAAC

Reverse complement sequence

GTTTGATAATGTGACATATAATCATATAGGCCAATTGTTCATGCTTGCTTGCAACGTTGAGCGCAAAATTTTGGAGAACCCAACGGGGCAACAAGCTATG[C/T]
TTGTGCCTCCTATCACTGATGTTTTACAGGAAGTTCAGAACAGTCCCCAAAATAAGAAGAACAATATGTTAGATATGTCACTTCCATCACTCGCAAATGA

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	26.40%	7.80%	5.97%	59.88%	NA
All Indica	2759	11.20%	1.70%	8.52%	78.58%	NA
All Japonica	1512	57.70%	14.30%	1.85%	26.12%	NA
Aus	269	9.70%	1.50%	5.20%	83.64%	NA
Indica I	595	25.50%	2.70%	15.97%	55.80%	NA
Indica II	465	10.50%	2.60%	10.54%	76.34%	NA
Indica III	913	2.50%	0.20%	0.99%	96.28%	NA
Indica Intermediate	786	10.80%	2.20%	10.43%	76.59%	NA
Temperate Japonica	767	73.10%	24.40%	0.91%	1.56%	NA
Tropical Japonica	504	32.50%	0.40%	2.98%	64.09%	NA
Japonica Intermediate	241	61.40%	11.20%	2.49%	24.90%	NA
VI/Aromatic	96	5.20%	87.50%	0.00%	7.29%	NA
Intermediate	90	37.80%	17.80%	5.56%	38.89%	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
vg0816260638	G -> A	LOC_Os08g26730.1	missense_variant ; p.Leu75Phe; MODERATE	nonsynonymous_codon ; L75F	Average:8.023; most accessible tissue: Callus, score: 35.198	possibly damaging	1.874	DELETERIOUS	0.01
vg0816260638	G -> DEL	LOC_Os08g26730.1	N	frameshift_variant	Average:8.023; most accessible tissue: Callus, score: 35.198	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816260638	2.30E-06	4.96E-27	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0816260638	NA	1.02E-07	Awn_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0816260638	NA	2.27E-08	mr1006	Jap_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
vg0816260638	NA	1.40E-07	mr1007	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
vg0816260638	NA	2.17E-08	mr1052	Jap_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

Showing 1 to 5 of 5 entries

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Search for Variation information by Variation ID:

Detailed information for vg0816260638:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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