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Detailed information for vg1127566128:

Variant ID: vg1127566128 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27566128
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


ATGATTTACAATCAGACTTGTTTTCTTTCTCTACTTTGTCTCTTAGTGCATTGTCATATTGCTCCACAAATTGCTTAAGTGTGGTTCTAGCATTAACATA[A/G]
CCATCAAAGAAGGCATTCACACTCTCACTCCTTTGCGACGAAGACATTCCAGCCCAAAATGTGTCTTTCACATAAGCCGGCACCCATAATTCCCTGTTAT

Reverse complement sequence

ATAACAGGGAATTATGGGTGCCGGCTTATGTGAAAGACACATTTTGGGCTGGAATGTCTTCGTCGCAAAGGAGTGAGAGTGTGAATGCCTTCTTTGATGG[T/C]
TATGTTAATGCTAGAACCACACTTAAGCAATTTGTGGAGCAATATGACAATGCACTAAGAGACAAAGTAGAGAAAGAAAACAAGTCTGATTGTAAATCAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.80% 11.80% 1.57% 46.87% NA
All Indica  2759 38.30% 5.00% 1.92% 54.77% NA
All Japonica  1512 44.80% 20.50% 0.99% 33.66% NA
Aus  269 14.90% 34.20% 1.49% 49.44% NA
Indica I  595 49.90% 3.40% 1.68% 45.04% NA
Indica II  465 65.80% 6.00% 1.29% 26.88% NA
Indica III  913 14.50% 4.20% 1.97% 79.41% NA
Indica Intermediate  786 40.80% 6.70% 2.42% 50.00% NA
Temperate Japonica  767 63.40% 1.60% 0.91% 34.16% NA
Tropical Japonica  504 17.90% 52.20% 0.60% 29.37% NA
Japonica Intermediate  241 42.30% 14.50% 2.07% 41.08% NA
VI/Aromatic  96 66.70% 0.00% 2.08% 31.25% NA
Intermediate  90 47.80% 16.70% 0.00% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127566128 A -> DEL LOC_Os11g45530.1 N frameshift_variant Average:21.193; most accessible tissue: Callus, score: 49.594 N N N N
vg1127566128 A -> G LOC_Os11g45530.1 synonymous_variant ; p.Gly424Gly; LOW synonymous_codon Average:21.193; most accessible tissue: Callus, score: 49.594 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127566128 NA 6.11E-14 mr1410 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
vg1127566128 3.11E-06 3.12E-06 mr1736 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
vg1127566128 NA 1.55E-14 mr1410_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
vg1127566128 NA 1.83E-11 mr1410_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
vg1127566128 NA 8.67E-06 mr1781_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