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Detailed information for vg0808191687:

Variant ID: vg0808191687 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8191687
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTACCCGCTCGCGATGATGTACTTGTCCGTGAACTCGCGCCACAGCTCGTTGTGCTCCAACGACTCCTCCTCCTCTGCTTTCTTGATCGCATCTTCCTC[A/C]
TCATCATCATCATCATCTGAATCGTCGGCGTACTCCGGTCGGTGATGACAGCCACAGGTGGTAGAGGAATCACGGTGGTCGGAGGAGGAGTCGCCGCCGC

Reverse complement sequence

GCGGCGGCGACTCCTCCTCCGACCACCGTGATTCCTCTACCACCTGTGGCTGTCATCACCGACCGGAGTACGCCGACGATTCAGATGATGATGATGATGA[T/G]
GAGGAAGATGCGATCAAGAAAGCAGAGGAGGAGGAGTCGTTGGAGCACAACGAGCTGTGGCGCGAGTTCACGGACAAGTACATCATCGCGAGCGGGTACG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.90% 6.90% 0.23% 0.00% NA
All Indica  2759 98.80% 1.20% 0.00% 0.00% NA
All Japonica  1512 89.40% 9.90% 0.73% 0.00% NA
Aus  269 53.20% 46.80% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.40% 1.60% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 0.00% NA
Temperate Japonica  767 95.30% 3.30% 1.43% 0.00% NA
Tropical Japonica  504 81.00% 19.00% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 0.00% 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
vg0808191687 A -> C LOC_Os08g13740.1 missense_variant ; p.Asp189Glu; MODERATE nonsynonymous_codon ; D189E Average:55.549; most accessible tissue: Zhenshan97 young leaf, score: 82.077 unknown unknown TOLERATED 0.44

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808191687 NA 5.16E-06 mr1057 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
vg0808191687 NA 9.47E-07 mr1345 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
vg0808191687 NA 4.70E-06 mr1417 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
vg0808191687 6.03E-06 NA mr1757 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
vg0808191687 1.89E-07 NA mr1549_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
vg0808191687 1.62E-07 NA mr1757_2 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