RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1214507607:

Variant ID: vg1214507607 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14507607
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGTCCGCCCTCTCCTTCGCTCCAGCTTCAGCCTTTAGGGGTCCAGCCAGTGGCAATGGAGGTTGGTTGCCTGCTACTCCCAGTGGCAGCCGCGACCGCA[A/G]
CAGCAGTTCCAGCAGCTTAGAGCCGGGCAGTGGCGAGACGTACCTGCAGGACTCCAAGAGCCGCTCAGAGGGACCAGGAGACGAGCAGGAGGACGCCTTC

Reverse complement sequence

GAAGGCGTCCTCCTGCTCGTCTCCTGGTCCCTCTGAGCGGCTCTTGGAGTCCTGCAGGTACGTCTCGCCACTGCCCGGCTCTAAGCTGCTGGAACTGCTG[T/C]
TGCGGTCGCGGCTGCCACTGGGAGTAGCAGGCAACCAACCTCCATTGCCACTGGCTGGACCCCTAAAGGCTGAAGCTGGAGCGAAGGAGAGGGCGGACAC

Allele Frequencies:

Search:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.80%	17.00%	0.59%	0.59%	NA
All Indica	2759	97.70%	1.70%	0.14%	0.43%	NA
All Japonica	1512	49.10%	48.40%	1.59%	0.86%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	97.00%	2.80%	0.00%	0.22%	NA
Indica III	913	98.00%	0.50%	0.33%	1.10%	NA
Indica Intermediate	786	96.70%	3.20%	0.00%	0.13%	NA
Temperate Japonica	767	19.80%	77.60%	1.69%	0.91%	NA
Tropical Japonica	504	85.70%	12.50%	0.99%	0.79%	NA
Japonica Intermediate	241	66.00%	30.70%	2.49%	0.83%	NA
VI/Aromatic	96	95.80%	3.10%	0.00%	1.04%	NA
Intermediate	90	74.40%	23.30%	0.00%	2.22%	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
vg1214507607	A -> DEL	N	N	silent_mutation	Average:64.852; most accessible tissue: Minghui63 young leaf, score: 86.199	N	N	N	N
vg1214507607	A -> G	LOC_Os12g25210.1	upstream_gene_variant ; 3704.0bp to feature; MODIFIER	silent_mutation	Average:64.852; most accessible tissue: Minghui63 young leaf, score: 86.199	N	N	N	N
vg1214507607	A -> G	LOC_Os12g25220.1	intron_variant ; MODIFIER	silent_mutation	Average:64.852; most accessible tissue: Minghui63 young leaf, score: 86.199	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214507607	NA	4.09E-06	mr1013	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
vg1214507607	NA	4.66E-35	mr1017	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
vg1214507607	3.07E-07	NA	mr1018	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
vg1214507607	NA	3.08E-10	mr1018	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
vg1214507607	3.11E-07	NA	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
vg1214507607	NA	1.07E-09	mr1019	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
vg1214507607	7.97E-06	4.68E-29	mr1022	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
vg1214507607	NA	3.65E-08	mr1022	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
vg1214507607	1.45E-08	3.48E-67	mr1023	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
vg1214507607	NA	2.31E-17	mr1023	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

Showing 1 to 10 of 64 entries

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Search for Variation information by Variation ID:

Detailed information for vg1214507607:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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