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Detailed information for vg0910945155:

Variant ID: vg0910945155 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10945155
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCATTTAACTAAACACTGAACTGATCTGTCCAATGATGCGTTTTTTTAGTTTTGATTCTGATGGAGATGTATGCAACAAAACTATCAACCCATCTCCGT[G/C]
AAGAAACAAATCAAAAAGGGCAGCTATAGCTATTTCCATAGTGGTTCTCGTGATGGCAATTGCTATACTTATTCTTGTGTATTTGGTTTGGAGACAGAGA

Reverse complement sequence

TCTCTGTCTCCAAACCAAATACACAAGAATAAGTATAGCAATTGCCATCACGAGAACCACTATGGAAATAGCTATAGCTGCCCTTTTTGATTTGTTTCTT[C/G]
ACGGAGATGGGTTGATAGTTTTGTTGCATACATCTCCATCAGAATCAAAACTAAAAAAACGCATCATTGGACAGATCAGTTCAGTGTTTAGTTAAATGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.90% 29.80% 0.36% 20.91% NA
All Indica  2759 68.70% 3.20% 0.47% 27.69% NA
All Japonica  1512 3.40% 84.50% 0.20% 11.84% NA
Aus  269 97.80% 1.10% 0.37% 0.74% NA
Indica I  595 76.30% 8.90% 0.17% 14.62% NA
Indica II  465 54.40% 1.70% 0.43% 43.44% NA
Indica III  913 72.70% 0.40% 0.33% 26.51% NA
Indica Intermediate  786 66.70% 2.80% 0.89% 29.64% NA
Temperate Japonica  767 0.90% 87.00% 0.26% 11.86% NA
Tropical Japonica  504 6.50% 88.70% 0.00% 4.76% NA
Japonica Intermediate  241 5.00% 68.00% 0.41% 26.56% NA
VI/Aromatic  96 70.80% 5.20% 0.00% 23.96% NA
Intermediate  90 37.80% 40.00% 0.00% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0910945155 G -> DEL N N silent_mutation Average:48.194; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N
vg0910945155 G -> C LOC_Os09g17890.1 intron_variant ; MODIFIER silent_mutation Average:48.194; most accessible tissue: Zhenshan97 young leaf, score: 71.065 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910945155 3.00E-06 NA mr1181 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
vg0910945155 NA 6.47E-07 mr1420 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
vg0910945155 NA 5.96E-08 mr1488 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
vg0910945155 NA 2.26E-10 mr1683 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
vg0910945155 NA 5.20E-09 mr1705_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