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Detailed information for vg0211794496:

Variant ID: vg0211794496 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11794496
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGGTGTCGTACTCCGCTCTTCTAGGATCAGACAGGGGAACACCAGTTGTTTGGTACAGAAGTTTTAAATGAGGCAGAAGAGAAAGTCAGAGCTGTCAGG[G/C]
AAAGATTGAGAATCGCGCAATCTCGACAAAGAAGCTATGCAGACAACCGCCGAAGGGAGCTCGTTTTCCAAGCAGGGGATTATGTGTATCTCCGTGTCAC

Reverse complement sequence

GTGACACGGAGATACACATAATCCCCTGCTTGGAAAACGAGCTCCCTTCGGCGGTTGTCTGCATAGCTTCTTTGTCGAGATTGCGCGATTCTCAATCTTT[C/G]
CCTGACAGCTCTGACTTTCTCTTCTGCCTCATTTAAAACTTCTGTACCAAACAACTGGTGTTCCCCTGTCTGATCCTAGAAGAGCGGAGTACGACACCTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.50% 0.60% 1.50% 2.48% NA
All Indica  2759 93.10% 0.90% 2.32% 3.70% NA
All Japonica  1512 99.50% 0.00% 0.20% 0.33% NA
Aus  269 95.20% 0.40% 1.12% 3.35% NA
Indica I  595 96.60% 0.80% 1.85% 0.67% NA
Indica II  465 93.10% 1.30% 2.80% 2.80% NA
Indica III  913 90.80% 1.00% 1.64% 6.57% NA
Indica Intermediate  786 93.00% 0.60% 3.18% 3.18% NA
Temperate Japonica  767 99.60% 0.00% 0.13% 0.26% NA
Tropical Japonica  504 99.40% 0.00% 0.20% 0.40% NA
Japonica Intermediate  241 99.20% 0.00% 0.41% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0211794496 G -> DEL LOC_Os02g20020.1 N frameshift_variant Average:14.719; most accessible tissue: Callus, score: 25.596 N N N N
vg0211794496 G -> C LOC_Os02g20020.1 missense_variant ; p.Glu1078Gln; MODERATE nonsynonymous_codon ; E1078Q Average:14.719; most accessible tissue: Callus, score: 25.596 possibly damaging 1.705 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211794496 1.07E-06 1.07E-06 mr1396 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