RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0917270003:

Variant ID: vg0917270003 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 17270003
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGGAGATTGAATTAATGAATAAGATCGAGGGGTGGGAATAAAAACCAAAGGTGCTCCATGCGGTTCGTCTCTGCTCGGCTCATAATAAGTGGTGTTGG[G/C]
TTATTTAAAAAACCAGCACATATAACCTTTTATAGGTACCGGTTTATTATAAAATCCGGTACAAATATTTAATGTGCCGGATTTTTAAATAAATTGACAA

Reverse complement sequence

TTGTCAATTTATTTAAAAATCCGGCACATTAAATATTTGTACCGGATTTTATAATAAACCGGTACCTATAAAAGGTTATATGTGCTGGTTTTTTAAATAA[C/G]
CCAACACCACTTATTATGAGCCGAGCAGAGACGAACCGCATGGAGCACCTTTGGTTTTTATTCCCACCCCTCGATCTTATTCATTAATTCAATCTCCACG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.60%	35.30%	0.19%	0.00%	NA
All Indica	2759	98.80%	1.10%	0.18%	0.00%	NA
All Japonica	1512	1.00%	99.00%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	96.30%	3.40%	0.22%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	98.50%	1.30%	0.25%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	36.70%	58.90%	4.44%	0.00%	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
vg0917270003	G -> C	LOC_Os09g28390-LOC_Os09g28400	intergenic_region ; MODIFIER	silent_mutation	Average:47.346; most accessible tissue: Callus, score: 92.008	N	N	N	N

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0917270003	NA	1.89E-103	mr1008	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
vg0917270003	NA	4.46E-101	mr1009	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
vg0917270003	NA	2.10E-68	mr1014	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
vg0917270003	NA	3.96E-56	mr1019	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
vg0917270003	NA	1.21E-10	mr1070	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
vg0917270003	NA	2.41E-33	mr1074	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
vg0917270003	NA	9.09E-39	mr1081	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
vg0917270003	NA	7.88E-48	mr1092	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
vg0917270003	NA	7.90E-56	mr1103	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
vg0917270003	NA	3.67E-10	mr1128	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 101 entries

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Search for Variation information by Variation ID:

Detailed information for vg0917270003:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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