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Detailed information for vg0910046375:

Variant ID: vg0910046375 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10046375
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTTCACAAAAGATAACCCATGTGCACCAGCAAAACGCTTGGAAATGAAGGAATGAGTTGCACCAGAATCAAACAATATTACTGCCGGTGTCGAGTTGA[T/C]
GGGAAATGTGCCCAATATAACCTCTGGTGCTGACTGTGCCTCCTCTGCAGACGCATGATTGACACGGGCCTGCACAAACTTGGGTCCAGCATGTCTTGGC

Reverse complement sequence

GCCAAGACATGCTGGACCCAAGTTTGTGCAGGCCCGTGTCAATCATGCGTCTGCAGAGGAGGCACAGTCAGCACCAGAGGTTATATTGGGCACATTTCCC[A/G]
TCAACTCGACACCGGCAGTAATATTGTTTGATTCTGGTGCAACTCATTCCTTCATTTCCAAGCGTTTTGCTGGTGCACATGGGTTATCTTTTGTGAAGCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.40% 15.40% 22.73% 2.50% NA
All Indica  2759 62.30% 7.10% 30.23% 0.43% NA
All Japonica  1512 61.20% 29.30% 2.65% 6.81% NA
Aus  269 32.30% 8.60% 57.99% 1.12% NA
Indica I  595 46.90% 7.70% 44.03% 1.34% NA
Indica II  465 64.70% 4.50% 30.75% 0.00% NA
Indica III  913 71.00% 9.60% 19.39% 0.00% NA
Indica Intermediate  786 62.30% 5.10% 32.06% 0.51% NA
Temperate Japonica  767 93.20% 1.60% 1.04% 4.17% NA
Tropical Japonica  504 7.90% 78.40% 4.76% 8.93% NA
Japonica Intermediate  241 71.00% 14.90% 3.32% 10.79% NA
VI/Aromatic  96 36.50% 35.40% 28.12% 0.00% NA
Intermediate  90 45.60% 35.60% 18.89% 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
vg0910046375 T -> DEL LOC_Os09g16430.1 N frameshift_variant Average:17.786; most accessible tissue: Minghui63 root, score: 31.271 N N N N
vg0910046375 T -> C LOC_Os09g16430.1 missense_variant ; p.Ile418Val; MODERATE nonsynonymous_codon ; I418V Average:17.786; most accessible tissue: Minghui63 root, score: 31.271 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910046375 NA 5.91E-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
vg0910046375 NA 2.54E-06 mr1471 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
vg0910046375 NA 3.11E-06 mr1642 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
vg0910046375 2.86E-06 1.26E-06 mr1686 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
vg0910046375 NA 6.06E-07 mr1047_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
vg0910046375 NA 4.12E-10 mr1471_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
vg0910046375 NA 3.77E-09 mr1642_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