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Detailed information for vg0138594460:

Variant ID: vg0138594460 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38594460
Reference Allele: CAlternative Allele: G
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAAGAGAGCGTAGAAATTCGAGTCACAACTCACAAGCTCAAATAAGCAAAGAAAACAAGAAATTAAGGCGTGCAGTAGATAATCGAGAGATGGAGATTG[C/G]
GATGAGCAGCAAGCGAGCGGAGGAGCTGGAGCAGCTGATCCAGCGGATGGAGCAGGCGGCGGCGCGTCGCCGGAAGACGCAGCCGGCGGGGAGCAAGCGC

Reverse complement sequence

GCGCTTGCTCCCCGCCGGCTGCGTCTTCCGGCGACGCGCCGCCGCCTGCTCCATCCGCTGGATCAGCTGCTCCAGCTCCTCCGCTCGCTTGCTGCTCATC[G/C]
CAATCTCCATCTCTCGATTATCTACTGCACGCCTTAATTTCTTGTTTTCTTTGCTTATTTGAGCTTGTGAGTTGTGACTCGAATTTCTACGCTCTCTTTC

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 47.90% 8.20% 5.12% 38.76% NA
All Indica  2759 42.90% 0.10% 3.04% 54.01% NA
All Japonica  1512 64.60% 25.30% 9.72% 0.46% NA
Aus  269 4.50% 0.00% 0.37% 95.17% NA
Indica I  595 36.60% 0.00% 4.37% 58.99% NA
Indica II  465 95.70% 0.00% 0.22% 4.09% NA
Indica III  913 13.40% 0.20% 3.07% 83.35% NA
Indica Intermediate  786 50.60% 0.00% 3.69% 45.67% NA
Temperate Japonica  767 60.20% 24.10% 15.38% 0.26% NA
Tropical Japonica  504 86.30% 10.70% 2.78% 0.20% NA
Japonica Intermediate  241 32.80% 59.30% 6.22% 1.66% NA
VI/Aromatic  96 32.30% 0.00% 5.21% 62.50% NA
Intermediate  90 70.00% 3.30% 5.56% 21.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0138594460 C -> G LOC_Os01g66480.1 missense_variant ; p.Ala4Gly; MODERATE nonsynonymous_codon ; A4G Average:75.543; most accessible tissue: Callus, score: 97.025 unknown unknown TOLERATED 1.00
vg0138594460 C -> DEL LOC_Os01g66480.1 N frameshift_variant Average:75.543; most accessible tissue: Callus, score: 97.025 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0138594460 3.09E-06 NA mr1334 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
vg0138594460 NA 6.19E-06 mr1173_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
vg0138594460 3.77E-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
vg0138594460 3.75E-06 1.08E-09 mr1691_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