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Detailed information for vg1208123893:

Variant ID: vg1208123893 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8123893
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTGATAAAGTGCCGGGTGATCTGTTTTCCTTGAAGGCCCTGATCTTTCAGCTTAATCATCCTCTCGATCAGTTCTACTGCTTGTGCAGCTTCGTCTCCC[A/G]
TTGGCAGTGAATTCCAAGTATCCCGATAAACTGGAGGAAGACAGGAGTACTCGGGAAGAACAGGCTCGGGGTTTTGAACATAAAACCAATTTGCGTGCCA

Reverse complement sequence

TGGCACGCAAATTGGTTTTATGTTCAAAACCCCGAGCCTGTTCTTCCCGAGTACTCCTGTCTTCCTCCAGTTTATCGGGATACTTGGAATTCACTGCCAA[T/C]
GGGAGACGAAGCTGCACAAGCAGTAGAACTGATCGAGAGGATGATTAAGCTGAAAGATCAGGGCCTTCAAGGAAAACAGATCACCCGGCACTTTATCAAG

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 44.80% 10.20% 22.18% 22.79% NA
All Indica  2759 36.60% 16.80% 35.56% 11.02% NA
All Japonica  1512 46.80% 0.50% 3.17% 49.47% NA
Aus  269 97.00% 0.40% 1.86% 0.74% NA
Indica I  595 50.30% 7.20% 32.94% 9.58% NA
Indica II  465 47.30% 18.30% 27.31% 7.10% NA
Indica III  913 22.30% 19.90% 42.72% 15.01% NA
Indica Intermediate  786 36.50% 19.60% 34.10% 9.80% NA
Temperate Japonica  767 73.70% 0.00% 1.96% 24.38% NA
Tropical Japonica  504 13.50% 1.60% 5.95% 78.97% NA
Japonica Intermediate  241 31.10% 0.00% 1.24% 67.63% NA
VI/Aromatic  96 91.70% 0.00% 2.08% 6.25% NA
Intermediate  90 56.70% 11.10% 13.33% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208123893 A -> DEL LOC_Os12g14270.1 N frameshift_variant Average:25.089; most accessible tissue: Minghui63 young leaf, score: 38.036 N N N N
vg1208123893 A -> G LOC_Os12g14270.1 missense_variant ; p.Met194Thr; MODERATE nonsynonymous_codon ; M194T Average:25.089; most accessible tissue: Minghui63 young leaf, score: 38.036 unknown unknown TOLERATED 0.10

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208123893 NA 6.50E-10 mr1425 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
vg1208123893 NA 9.24E-08 mr1425 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
vg1208123893 6.84E-06 NA mr1539_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
vg1208123893 4.43E-06 9.47E-09 mr1539_2 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
vg1208123893 4.59E-07 NA mr1540_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
vg1208123893 5.24E-07 3.51E-10 mr1540_2 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
vg1208123893 NA 8.91E-07 mr1568_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
vg1208123893 3.11E-06 NA mr1732_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
vg1208123893 3.26E-06 5.94E-09 mr1732_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
vg1208123893 NA 5.39E-07 mr1910_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