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Detailed information for vg0517761858:

Variant ID: vg0517761858 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17761858
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCCCATGAAAGCCACAATTTCGAAATTCATACCCCATGAAAGCCACAATTTCGGTCGTTGCTCATAGAACCGCATACTTACCAAACTTTCTTGTATCCT[G/C]
TTCCTTGTGAACCTCCACGACCTGCTATTGTAAAAAATGGAGAAAACAATTGAATAGTACAACGTAAATCGTAGTTGATCAAATTTGATGACAATTTAGC

Reverse complement sequence

GCTAAATTGTCATCAAATTTGATCAACTACGATTTACGTTGTACTATTCAATTGTTTTCTCCATTTTTTACAATAGCAGGTCGTGGAGGTTCACAAGGAA[C/G]
AGGATACAAGAAAGTTTGGTAAGTATGCGGTTCTATGAGCAACGACCGAAATTGTGGCTTTCATGGGGTATGAATTTCGAAATTGTGGCTTTCATGGGGT

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 41.50% 2.40% 5.12% 51.02% NA
All Indica  2759 19.60% 0.10% 7.79% 72.53% NA
All Japonica  1512 84.10% 7.10% 0.53% 8.33% NA
Aus  269 4.10% 0.00% 4.46% 91.45% NA
Indica I  595 18.50% 0.00% 12.27% 69.24% NA
Indica II  465 36.60% 0.00% 6.45% 56.99% NA
Indica III  913 12.70% 0.20% 5.15% 81.93% NA
Indica Intermediate  786 18.30% 0.10% 8.27% 73.28% NA
Temperate Japonica  767 97.10% 0.10% 0.13% 2.61% NA
Tropical Japonica  504 58.30% 20.40% 1.19% 20.04% NA
Japonica Intermediate  241 96.30% 1.20% 0.41% 2.07% NA
VI/Aromatic  96 93.80% 0.00% 0.00% 6.25% NA
Intermediate  90 53.30% 3.30% 7.78% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0517761858 G -> DEL LOC_Os05g30670.1 N frameshift_variant Average:7.48; most accessible tissue: Callus, score: 24.07 N N N N
vg0517761858 G -> C LOC_Os05g30670.1 missense_variant ; p.Thr67Arg; MODERATE nonsynonymous_codon ; T67R Average:7.48; most accessible tissue: Callus, score: 24.07 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517761858 NA 2.74E-06 mr1076 Jap_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
vg0517761858 NA 4.19E-06 mr1082 Jap_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
vg0517761858 NA 6.31E-06 mr1083 Jap_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
vg0517761858 NA 1.23E-06 mr1226 Jap_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
vg0517761858 2.09E-06 5.35E-08 mr1227 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
vg0517761858 NA 1.54E-08 mr1082_2 Jap_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
vg0517761858 NA 1.61E-08 mr1083_2 Jap_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
vg0517761858 NA 6.96E-06 mr1104_2 Jap_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
vg0517761858 NA 7.14E-07 mr1226_2 Jap_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
vg0517761858 NA 6.20E-06 mr1408_2 Jap_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