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Detailed information for vg0714479069:

Variant ID: vg0714479069 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 14479069
Reference Allele: AAlternative Allele: G,AGAG
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGACCACGATCTCGAGGTTCACTATCACCCTGGCAAGGCAAACGTCGTGGCCGACGCTTTGAGTCGTAAGAGCCATTGCAATCATCTGAGAATGGAAGG[A/G,AGAG]
ATGGCTCCTGAGCTTAAAGAGGAATATGCCCAGCTAAACCTACATATAGTGCCTCGTGGACGGATAAACACCCTTGACATTCAACCTCTTTTGAGAACCC

Reverse complement sequence

GGGTTCTCAAAAGAGGTTGAATGTCAAGGGTGTTTATCCGTCCACGAGGCACTATATGTAGGTTTAGCTGGGCATATTCCTCTTTAAGCTCAGGAGCCAT[T/C,CTCT]
CCTTCCATTCTCAGATGATTGCAATGGCTCTTACGACTCAAAGCGTCGGCCACGACGTTTGCCTTGCCAGGGTGATAGTGAACCTCGAGATCGTGGTCCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.60% 32.40% 7.34% 18.71% NA
All Indica  2759 24.10% 47.10% 9.46% 19.35% NA
All Japonica  1512 75.20% 5.00% 3.44% 16.34% NA
Aus  269 28.30% 41.30% 8.18% 22.30% NA
Indica I  595 26.20% 61.00% 2.52% 10.25% NA
Indica II  465 28.60% 44.10% 12.90% 14.41% NA
Indica III  913 18.70% 40.00% 10.95% 30.34% NA
Indica Intermediate  786 26.00% 46.70% 10.94% 16.41% NA
Temperate Japonica  767 77.70% 6.10% 2.48% 13.69% NA
Tropical Japonica  504 79.80% 3.00% 1.59% 15.67% NA
Japonica Intermediate  241 57.70% 5.80% 10.37% 26.14% NA
VI/Aromatic  96 43.80% 19.80% 8.33% 28.12% NA
Intermediate  90 50.00% 27.80% 4.44% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0714479069 A -> DEL LOC_Os07g25340.1 N frameshift_variant Average:17.905; most accessible tissue: Callus, score: 40.135 N N N N
vg0714479069 A -> AGAG LOC_Os07g25340.1 inframe_insertion ; p.Gly889_Met890insGlu; MODERATE N Average:17.905; most accessible tissue: Callus, score: 40.135 N N N N
vg0714479069 A -> G LOC_Os07g25340.1 synonymous_variant ; p.Gly889Gly; LOW synonymous_codon Average:17.905; most accessible tissue: Callus, score: 40.135 N N N N
vg0714479069 A -> G LOC_Os07g25340.1 synonymous_variant ; p.Gly889Gly; LOW nonsynonymous_codon ; G889R Average:17.905; most accessible tissue: Callus, score: 40.135 probably damaging 2.199 TOLERATED 0.10
vg0714479069 A -> G LOC_Os07g25340.1 synonymous_variant ; p.Gly889Gly; LOW nonsynonymous_codon ; G889E Average:17.905; most accessible tissue: Callus, score: 40.135 benign 0.626 TOLERATED 0.18

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714479069 2.19E-06 2.62E-07 mr1428 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