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Detailed information for vg0106301158:

Variant ID: vg0106301158 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6301158
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTTTTTTCCCTCCATCTGAGTATAATGGCACCCTTTTTTCCCTCCAGAAACAGAGCAACAAACGGCGGCGCACGGCAATGAGGATGTTTGTGGGCCAT[T/C]
TTCATTGGCATGGGCTGACCGCGAGCCCGTTTGACCGCCTTATTCGTTGCGCTCGTGCGACCGCCGCCGCCGCTGTGGAAGCCGTCGTTGTTGAGGACGG

Reverse complement sequence

CCGTCCTCAACAACGACGGCTTCCACAGCGGCGGCGGCGGTCGCACGAGCGCAACGAATAAGGCGGTCAAACGGGCTCGCGGTCAGCCCATGCCAATGAA[A/G]
ATGGCCCACAAACATCCTCATTGCCGTGCGCCGCCGTTTGTTGCTCTGTTTCTGGAGGGAAAAAAGGGTGCCATTATACTCAGATGGAGGGAAAAAAAGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 1.60% 1.95% 0.34% NA
All Indica  2759 99.30% 0.10% 0.07% 0.58% NA
All Japonica  1512 89.20% 5.00% 5.89% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 98.40% 0.00% 0.00% 1.64% NA
Indica Intermediate  786 99.60% 0.00% 0.25% 0.13% NA
Temperate Japonica  767 79.50% 9.80% 10.69% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 97.90% 0.00% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0106301158 T -> DEL N N silent_mutation Average:52.52; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0106301158 T -> C LOC_Os01g11700.1 upstream_gene_variant ; 3644.0bp to feature; MODIFIER silent_mutation Average:52.52; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0106301158 T -> C LOC_Os01g11700.2 upstream_gene_variant ; 3644.0bp to feature; MODIFIER silent_mutation Average:52.52; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0106301158 T -> C LOC_Os01g11670.1 downstream_gene_variant ; 3482.0bp to feature; MODIFIER silent_mutation Average:52.52; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0106301158 T -> C LOC_Os01g11690.1 downstream_gene_variant ; 2404.0bp to feature; MODIFIER silent_mutation Average:52.52; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N
vg0106301158 T -> C LOC_Os01g11680.1 intron_variant ; MODIFIER silent_mutation Average:52.52; most accessible tissue: Minghui63 young leaf, score: 75.006 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106301158 8.40E-06 NA mr1296 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
vg0106301158 5.01E-08 5.01E-08 mr1371_2 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
vg0106301158 3.89E-06 3.89E-06 mr1445_2 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