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Detailed information for vg0716554289:

Variant ID: vg0716554289 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16554289
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCATCACGCCCACCCTTGCCTGGATGCGTCAACTAGAGGAAAGCTACACTACAAGCCCAGCCGTTGCCCACGCTAGCTTGTGGTAAGTACGAGGAATT[G/C]
TTCTAGGGTTTCCCGCGAACCGGTCCTCAAGTGCCATGGGCGCGACCATCACAACCATGCACCCACAGCCCACTAGATGGTATATTTTAATTGACTAACA

Reverse complement sequence

TGTTAGTCAATTAAAATATACCATCTAGTGGGCTGTGGGTGCATGGTTGTGATGGTCGCGCCCATGGCACTTGAGGACCGGTTCGCGGGAAACCCTAGAA[C/G]
AATTCCTCGTACTTACCACAAGCTAGCGTGGGCAACGGCTGGGCTTGTAGTGTAGCTTTCCTCTAGTTGACGCATCCAGGCAAGGGTGGGCGTGATGGTG

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 44.00% 7.40% 8.74% 39.89% NA
All Indica  2759 25.10% 1.90% 12.03% 60.93% NA
All Japonica  1512 80.40% 18.30% 0.73% 0.60% NA
Aus  269 15.60% 4.50% 20.82% 59.11% NA
Indica I  595 45.20% 0.20% 5.38% 49.24% NA
Indica II  465 7.30% 0.40% 9.46% 82.80% NA
Indica III  913 19.20% 0.80% 18.18% 61.88% NA
Indica Intermediate  786 27.40% 5.50% 11.45% 55.73% NA
Temperate Japonica  767 93.90% 4.60% 0.91% 0.65% NA
Tropical Japonica  504 56.70% 42.50% 0.60% 0.20% NA
Japonica Intermediate  241 87.10% 11.20% 0.41% 1.24% NA
VI/Aromatic  96 85.40% 0.00% 11.46% 3.12% NA
Intermediate  90 50.00% 10.00% 3.33% 36.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0716554289 G -> DEL N N silent_mutation Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529 N N N N
vg0716554289 G -> C LOC_Os07g28350.1 downstream_gene_variant ; 4310.0bp to feature; MODIFIER silent_mutation Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529 N N N N
vg0716554289 G -> C LOC_Os07g28360.1 intron_variant ; MODIFIER silent_mutation Average:36.945; most accessible tissue: Zhenshan97 flag leaf, score: 82.529 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716554289 1.62E-07 NA mr1705_2 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
vg0716554289 1.59E-06 7.34E-10 mr1705_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