RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1013489724:

Variant ID: vg1013489724 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13489724
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

TGATTGATATACCCAAAAACCGAAAACTTTTAGCGGAAATAGAAGTTACCCTCGAAATCGACGGAAGTCGGTCTGACCGAGATTAATCTGCCGGTCTGAC[C/T]
GAAGCGTAGCCGCCGGTCTGACCGGTGTTGATCTTCTGGTTGGACTGCCCTGGAATCCCTGCCGCGCCTATTGTCGCCGCCGGTCTGACCGCAGGTCACC

Reverse complement sequence

GGTGACCTGCGGTCAGACCGGCGGCGACAATAGGCGCGGCAGGGATTCCAGGGCAGTCCAACCAGAAGATCAACACCGGTCAGACCGGCGGCTACGCTTC[G/A]
GTCAGACCGGCAGATTAATCTCGGTCAGACCGACTTCCGTCGATTTCGAGGGTAACTTCTATTTCCGCTAAAAGTTTTCGGTTTTTGGGTATATCAATCA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.20%	24.70%	0.08%	0.00%	NA
All Indica	2759	98.90%	1.00%	0.11%	0.00%	NA
All Japonica	1512	32.20%	67.80%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.30%	0.13%	0.00%	NA
Temperate Japonica	767	5.70%	94.30%	0.00%	0.00%	NA
Tropical Japonica	504	65.90%	34.10%	0.00%	0.00%	NA
Japonica Intermediate	241	46.10%	53.90%	0.00%	0.00%	NA
VI/Aromatic	96	18.80%	81.20%	0.00%	0.00%	NA
Intermediate	90	56.70%	42.20%	1.11%	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
vg1013489724	C -> T	LOC_Os10g26040.1	missense_variant ; p.Gly74Ser; MODERATE	nonsynonymous_codon ; G74S	Average:47.876; most accessible tissue: Minghui63 root, score: 68.289	unknown	unknown	TOLERATED	0.11

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
vg1013489724	NA	5.69E-09	mr1005	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
vg1013489724	NA	5.92E-09	mr1275	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
vg1013489724	NA	1.28E-23	mr1300	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
vg1013489724	1.84E-07	NA	mr1301	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
vg1013489724	NA	8.15E-15	mr1301	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
vg1013489724	NA	9.84E-36	mr1310	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
vg1013489724	NA	2.08E-07	mr1364	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
vg1013489724	NA	3.32E-14	mr1410	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
vg1013489724	NA	2.16E-11	mr1410	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
vg1013489724	NA	9.56E-08	mr1424	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 22 entries

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Search for Variation information by Variation ID:

Detailed information for vg1013489724:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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