RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1006376447:

Variant ID: vg1006376447 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6376447
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCACACATGTCGCCATGCCCGAAGTATCACCATGATACTGCAAAGGGGGTAATCGTGACAAGACCCTCTGCATAACCCTCCCCTAACCATCCACACCA[C/T]
GCTAAGGTTTCACCCCCACCCCTCAAAAGGCAGTGGGCGGTCCCGTCTTGCGCCGCGGTGAATCCGGCAGCTGGACAACCGGACACCCCCGCCGACCCAA

Reverse complement sequence

TTGGGTCGGCGGGGGTGTCCGGTTGTCCAGCTGCCGGATTCACCGCGGCGCAAGACGGGACCGCCCACTGCCTTTTGAGGGGTGGGGGTGAAACCTTAGC[G/A]
TGGTGTGGATGGTTAGGGGAGGGTTATGCAGAGGGTCTTGTCACGATTACCCCCTTTGCAGTATCATGGTGATACTTCGGGCATGGCGACATGTGTGGAA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.50%	20.50%	0.04%	0.00%	NA
All Indica	2759	65.70%	34.20%	0.07%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	14.30%	85.50%	0.17%	0.00%	NA
Indica II	465	84.10%	15.90%	0.00%	0.00%	NA
Indica III	913	85.90%	14.10%	0.00%	0.00%	NA
Indica Intermediate	786	70.40%	29.50%	0.13%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	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
vg1006376447	C -> T	LOC_Os10g11506.1	intron_variant ; MODIFIER	silent_mutation	Average:61.614; most accessible tissue: Zhenshan97 flag leaf, score: 76.925	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
vg1006376447	6.28E-09	5.98E-41	mr1026	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
vg1006376447	8.40E-09	9.33E-23	mr1026	Ind_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
vg1006376447	NA	1.39E-07	mr1113	Ind_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
vg1006376447	NA	9.92E-07	mr1114	Ind_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
vg1006376447	NA	4.03E-06	mr1116	Ind_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
vg1006376447	NA	1.16E-17	mr1118	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
vg1006376447	3.32E-08	7.87E-21	mr1118	Ind_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
vg1006376447	NA	6.51E-07	mr1120	Ind_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
vg1006376447	3.44E-08	1.15E-37	mr1161	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
vg1006376447	4.34E-08	1.04E-20	mr1161	Ind_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 33 entries

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Search for Variation information by Variation ID:

Detailed information for vg1006376447:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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