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Detailed information for vg0118270461:

Variant ID: vg0118270461 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18270461
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


CTCGACCATCTGAGGTTGCGGTGCGAGAGATTACTACGCACTGGTTTGAGGACCAGCGAACGTGTAGAATTATCTCTCGGACACCAATGGAGGTTGCGGT[A/G]
CGAGAGATTGCTACGCACTGGTTCGAGGACCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGT

Reverse complement sequence

ACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGGTCCTCGAACCAGTGCGTAGCAATCTCTCG[T/C]
ACCGCAACCTCCATTGGTGTCCGAGAGATAATTCTACACGTTCGCTGGTCCTCAAACCAGTGCGTAGTAATCTCTCGCACCGCAACCTCAGATGGTCGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.90% 34.70% 2.48% 1.90% NA
All Indica  2759 92.10% 1.90% 3.08% 2.90% NA
All Japonica  1512 8.30% 91.60% 0.00% 0.13% NA
Aus  269 61.30% 24.20% 11.52% 2.97% NA
Indica I  595 91.30% 0.30% 5.55% 2.86% NA
Indica II  465 95.10% 3.70% 0.65% 0.65% NA
Indica III  913 94.30% 0.40% 1.75% 3.50% NA
Indica Intermediate  786 88.50% 3.70% 4.20% 3.56% NA
Temperate Japonica  767 4.60% 95.40% 0.00% 0.00% NA
Tropical Japonica  504 6.30% 93.30% 0.00% 0.40% NA
Japonica Intermediate  241 24.10% 75.90% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 44.40% 54.40% 1.11% 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
vg0118270461 A -> G LOC_Os01g33180.1 synonymous_variant ; p.Val5Val; LOW synonymous_codon Average:54.568; most accessible tissue: Minghui63 young leaf, score: 76.82 N N N N
vg0118270461 A -> DEL LOC_Os01g33180.1 N frameshift_variant Average:54.568; most accessible tissue: Minghui63 young leaf, score: 76.82 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118270461 NA 3.24E-19 mr1021 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
vg0118270461 NA 1.07E-44 mr1092 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
vg0118270461 NA 5.85E-15 mr1228 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
vg0118270461 NA 5.36E-19 mr1242 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
vg0118270461 NA 5.45E-51 mr1519 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
vg0118270461 NA 6.15E-12 mr1744 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
vg0118270461 NA 5.35E-08 mr1299_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
vg0118270461 NA 4.88E-09 mr1379_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
vg0118270461 NA 1.52E-52 mr1519_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
vg0118270461 NA 9.79E-08 mr1700_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
vg0118270461 NA 2.03E-07 mr1727_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
vg0118270461 NA 3.84E-06 mr1840_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