RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0807117547:

Variant ID: vg0807117547 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7117547
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.14, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGAGGAGTGGTTCCTGGAGCAAGATCTATCCGGAACTCAATCTCTCGCTTGGGCGGCATACCGCGTAGTTCTTCCGGAAACACATCTCCGAACTCTCT[A/G]
ACGATGGGGGTTTCCGACAGTCCTATCTGATGAAGTTCTGAACTGCCGACAGAGGTTGAGGGTGCAAAGAAAACAACCGGTTGTTCCGGCCCTCGGTACA

Reverse complement sequence

TGTACCGAGGGCCGGAACAACCGGTTGTTTTCTTTGCACCCTCAACCTCTGTCGGCAGTTCAGAACTTCATCAGATAGGACTGTCGGAAACCCCCATCGT[T/C]
AGAGAGTTCGGAGATGTGTTTCCGGAAGAACTACGCGGTATGCCGCCCAAGCGAGAGATTGAGTTCCGGATAGATCTTGCTCCAGGAACCACTCCTCTGT

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	37.90%	11.50%	19.09%	31.53%	NA
All Indica	2759	10.50%	17.70%	22.44%	49.29%	NA
All Japonica	1512	94.80%	0.30%	1.19%	3.64%	NA
Aus	269	7.10%	11.90%	61.71%	19.33%	NA
Indica I	595	25.00%	6.60%	12.94%	55.46%	NA
Indica II	465	9.70%	23.00%	28.60%	38.71%	NA
Indica III	913	1.40%	22.00%	22.34%	54.22%	NA
Indica Intermediate	786	10.70%	18.10%	26.08%	45.17%	NA
Temperate Japonica	767	93.50%	0.00%	0.39%	6.13%	NA
Tropical Japonica	504	96.20%	0.60%	1.98%	1.19%	NA
Japonica Intermediate	241	96.30%	0.80%	2.07%	0.83%	NA
VI/Aromatic	96	5.20%	10.40%	83.33%	1.04%	NA
Intermediate	90	46.70%	7.80%	21.11%	24.44%	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
vg0807117547	A -> G	LOC_Os08g12080.1	synonymous_variant ; p.Val739Val; LOW	synonymous_codon	Average:34.742; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg0807117547	A -> G	LOC_Os08g12080.1	synonymous_variant ; p.Val739Val; LOW	nonsynonymous_codon ; V739L	Average:34.742; most accessible tissue: Minghui63 flag leaf, score: 75.341	benign	1.363	DELETERIOUS	0.00
vg0807117547	A -> DEL	LOC_Os08g12080.1	N	frameshift_variant	Average:34.742; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

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
vg0807117547	6.38E-08	1.45E-09	mr1100	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
vg0807117547	NA	1.61E-89	mr1140	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
vg0807117547	NA	5.99E-07	mr1140	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
vg0807117547	1.04E-06	6.35E-98	mr1203	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
vg0807117547	NA	1.22E-06	mr1203	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
vg0807117547	4.72E-06	2.73E-90	mr1395	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
vg0807117547	8.87E-06	8.70E-08	mr1395	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
vg0807117547	NA	3.91E-35	mr1402	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
vg0807117547	NA	8.46E-39	mr1480	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
vg0807117547	NA	1.67E-77	mr1613	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 19 entries

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Search for Variation information by Variation ID:

Detailed information for vg0807117547:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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