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Detailed information for vg1125103237:

Variant ID: vg1125103237 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25103237
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTAGAAATGCAGATACTTACTCATCACCCCGAGGTTTCAGCGCGATCTTTCGACCCCGCGGAGGTACTTTTAGTGCAGTTCTTGAGCCCTTCTTCCTC[C/G]
CTCTTTTATTTGGTGGCGCACTGCTCATGCCACTTCCAGCAATATTGGTGGCTTGGGAGGCATTATCAGTATTGCTACTATTACCAGCACAAAGTCTTTG

Reverse complement sequence

CAAAGACTTTGTGCTGGTAATAGTAGCAATACTGATAATGCCTCCCAAGCCACCAATATTGCTGGAAGTGGCATGAGCAGTGCGCCACCAAATAAAAGAG[G/C]
GAGGAAGAAGGGCTCAAGAACTGCACTAAAAGTACCTCCGCGGGGTCGAAAGATCGCGCTGAAACCTCGGGGTGATGAGTAAGTATCTGCATTTCTAGAA

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 95.50% 0.10% 4.34% 0.02% NA
All Indica  2759 99.90% 0.00% 0.11% 0.00% NA
All Japonica  1512 86.50% 0.40% 13.03% 0.07% NA
Aus  269 98.90% 0.00% 1.12% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.25% 0.00% NA
Temperate Japonica  767 78.00% 0.70% 21.25% 0.13% NA
Tropical Japonica  504 98.20% 0.00% 1.79% 0.00% NA
Japonica Intermediate  241 89.20% 0.40% 10.37% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 98.90% 0.00% 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
vg1125103237 C -> DEL LOC_Os11g41770.1 N frameshift_variant Average:16.49; most accessible tissue: Callus, score: 38.406 N N N N
vg1125103237 C -> G LOC_Os11g41770.1 missense_variant ; p.Gly84Ala; MODERATE nonsynonymous_codon ; G84A Average:16.49; most accessible tissue: Callus, score: 38.406 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125103237 5.52E-07 NA mr1238 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
vg1125103237 4.18E-07 NA mr1309 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
vg1125103237 9.80E-08 2.38E-06 mr1484 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
vg1125103237 6.55E-07 5.61E-06 mr1841 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
vg1125103237 1.37E-06 NA mr1900 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
vg1125103237 1.15E-07 2.74E-06 mr1238_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
vg1125103237 9.36E-07 9.36E-07 mr1484_2 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
vg1125103237 1.89E-07 4.81E-06 mr1841_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
vg1125103237 1.09E-07 2.39E-06 mr1900_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
vg1125103237 4.20E-07 4.21E-07 mr1945_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
vg1125103237 7.06E-06 NA mr1959_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