\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1102140175:

Variant ID: vg1102140175 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2140175
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTTGCTTAACTCTATGTTTGTGCACTCACATGTTTGCTGACAATTCAAAACAAGAATTTGATAAATCATAGCATAACATTTTGTAAATAACTGAGACT[T/A]
CGCCAAGTTGAGAATAATATTAAGAAATAAAAGCCGGATGCTCAAATGAGATTTCGAGGATTCTTACACGAAATTATCATGAAGCGTTGCAATATCAGGG

Reverse complement sequence

CCCTGATATTGCAACGCTTCATGATAATTTCGTGTAAGAATCCTCGAAATCTCATTTGAGCATCCGGCTTTTATTTCTTAATATTATTCTCAACTTGGCG[A/T]
AGTCTCAGTTATTTACAAAATGTTATGCTATGATTTATCAAATTCTTGTTTTGAATTGTCAGCAAACATGTGAGTGCACAAACATAGAGTTAAGCAAAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.40% 2.30% 0.30% 0.00% NA
All Indica  2759 95.80% 3.70% 0.47% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 82.40% 15.70% 1.94% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 96.40% 3.30% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg1102140175 T -> A LOC_Os11g04980.1 intron_variant ; MODIFIER silent_mutation Average:48.747; most accessible tissue: Callus, score: 76.889 N N N N
vg1102140175 T -> A LOC_Os11g04980.2 intron_variant ; MODIFIER silent_mutation Average:48.747; most accessible tissue: Callus, score: 76.889 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102140175 9.08E-06 9.08E-06 mr1396 Ind_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
vg1102140175 NA 2.45E-06 mr1415 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
vg1102140175 NA 2.45E-06 mr1567 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
vg1102140175 NA 4.85E-06 mr1588_2 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
vg1102140175 NA 1.16E-08 mr1806_2 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
vg1102140175 NA 2.20E-08 mr1828_2 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