RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0720025560:

Variant ID: vg0720025560 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20025560
Reference Allele: G	Alternative Allele: T,A
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CATAGCATGTTGAGAACGCGGTTTTGGGTATGTCCCCGGTTCTAATTTTCAATTGGTGGTATCCTGACCGAAGGTCAATCTTAGAGAACACCTTAGCTCC[G/T,A]
TTGAGTTGATCAAAAAGATCATCAATCCGTGGTAGTGGATACTTGTTTTTAATAGTTACTTCGTTCAGTGATCGGTAGTCTACACACATTCTCATGCTAC

Reverse complement sequence

GTAGCATGAGAATGTGTGTAGACTACCGATCACTGAACGAAGTAACTATTAAAAACAAGTATCCACTACCACGGATTGATGATCTTTTTGATCAACTCAA[C/A,T]
GGAGCTAAGGTGTTCTCTAAGATTGACCTTCGGTCAGGATACCACCAATTGAAAATTAGAACCGGGGACATACCCAAAACCGCGTTCTCAACATGCTATG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.90%	20.80%	9.75%	5.97%	A: 0.51%
All Indica	2759	92.80%	1.00%	4.97%	0.40%	A: 0.87%
All Japonica	1512	7.90%	62.00%	12.70%	17.39%	NA
Aus	269	79.90%	0.40%	19.70%	0.00%	NA
Indica I	595	93.30%	0.70%	5.88%	0.17%	NA
Indica II	465	88.60%	1.70%	7.74%	1.08%	A: 0.86%
Indica III	913	96.30%	0.20%	1.64%	0.00%	A: 1.86%
Indica Intermediate	786	90.80%	1.70%	6.49%	0.64%	A: 0.38%
Temperate Japonica	767	1.30%	94.00%	0.52%	4.17%	NA
Tropical Japonica	504	19.80%	12.10%	33.73%	34.33%	NA
Japonica Intermediate	241	3.70%	64.70%	7.47%	24.07%	NA
VI/Aromatic	96	32.30%	2.10%	62.50%	3.12%	NA
Intermediate	90	54.40%	18.90%	21.11%	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
vg0720025560	G -> DEL	LOC_Os07g33500.1	N	frameshift_variant	Average:31.856; most accessible tissue: Minghui63 young leaf, score: 56.213	N	N	N	N
vg0720025560	G -> A	LOC_Os07g33500.1	synonymous_variant ; p.Asn623Asn; LOW	synonymous_codon	Average:31.856; most accessible tissue: Minghui63 young leaf, score: 56.213	N	N	N	N
vg0720025560	G -> T	LOC_Os07g33500.1	missense_variant ; p.Asn623Lys; MODERATE	nonsynonymous_codon	Average:31.856; most accessible tissue: Minghui63 young leaf, score: 56.213	possibly damaging	-1.525	TOLERATED	1.00

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720025560	NA	4.98E-37	Grain_thickness	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
vg0720025560	NA	1.09E-54	Grain_width	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
vg0720025560	NA	7.92E-41	mr1093	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
vg0720025560	NA	7.99E-08	mr1271	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
vg0720025560	NA	6.14E-17	mr1308	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
vg0720025560	NA	2.52E-89	mr1334	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
vg0720025560	NA	5.93E-15	mr1401	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
vg0720025560	NA	3.16E-06	mr1422	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
vg0720025560	NA	3.28E-06	mr1443	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
vg0720025560	2.46E-06	4.70E-26	mr1679	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 10 of 31 entries

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Search for Variation information by Variation ID:

Detailed information for vg0720025560:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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