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Detailed information for vg1111322133:

Variant ID: vg1111322133 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 11322133
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.57, C: 0.41, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


TGCCGACGTCGGCTGGTTTTCTGATGAGCCCTTGAAGGAGAGTTGAAGTCCTGGGGGCATTATAGCCAATAACAGGAGGAGATGGTCCACCCCCGTTTGG[A/C]
ATCAGCCCCAGGGCATACTCAATATTTCTGCCACTATTGCTCTGGCGAGGAGGAGAGAACTCTGTTGTCTACAAATTAAAAGGAAAATTAGTCAAGATTA

Reverse complement sequence

TAATCTTGACTAATTTTCCTTTTAATTTGTAGACAACAGAGTTCTCTCCTCCTCGCCAGAGCAATAGTGGCAGAAATATTGAGTATGCCCTGGGGCTGAT[T/G]
CCAAACGGGGGTGGACCATCTCCTCCTGTTATTGGCTATAATGCCCCCAGGACTTCAACTCTCCTTCAAGGGCTCATCAGAAAACCAGCCGACGTCGGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.90% 33.90% 0.17% 0.00% NA
All Indica  2759 98.00% 1.80% 0.22% 0.00% NA
All Japonica  1512 5.00% 94.80% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.50% 2.40% 0.17% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.50% 0.40% 0.11% 0.00% NA
Indica Intermediate  786 96.20% 3.30% 0.51% 0.00% NA
Temperate Japonica  767 3.70% 96.20% 0.13% 0.00% NA
Tropical Japonica  504 8.30% 91.50% 0.20% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 58.90% 41.10% 0.00% 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
vg1111322133 A -> C LOC_Os11g19650.1 missense_variant ; p.Ile226Met; MODERATE nonsynonymous_codon ; I226M Average:42.294; most accessible tissue: Minghui63 young leaf, score: 60.103 probably damaging 2.635 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1111322133 NA 1.46E-06 mr1156 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
vg1111322133 4.22E-06 NA mr1624 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