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Detailed information for vg1124874746:

Variant ID: vg1124874746 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24874746
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGCTTCACACCGCTGCACCATGTCGCAGGCGTCTTTGAGCGCGGTCGGCCAGAAAAACCCTTGTCGAAAAGCTTTTCCTACCAACGTCCGTCCGCCGG[T/C]
GTGTGACCCGCAGATCCCTTCATGTATGTCCAGGAGGAGATGTTTGCCGTCATCAGATGAGATGCATTTGAGAAGTAGTCCGTTTGGTGCCTTTTTGTAC

Reverse complement sequence

GTACAAAAAGGCACCAAACGGACTACTTCTCAAATGCATCTCATCTGATGACGGCAAACATCTCCTCCTGGACATACATGAAGGGATCTGCGGGTCACAC[A/G]
CCGGCGGACGGACGTTGGTAGGAAAAGCTTTTCGACAAGGGTTTTTCTGGCCGACCGCGCTCAAAGACGCCTGCGACATGGTGCAGCGGTGTGAAGCCTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.40% 13.50% 0.30% 0.72% NA
All Indica  2759 99.20% 0.70% 0.00% 0.07% NA
All Japonica  1512 57.00% 40.00% 0.86% 2.12% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.40% 0.00% 0.25% NA
Temperate Japonica  767 21.10% 73.10% 1.69% 4.04% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 85.90% 13.70% 0.00% 0.41% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 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
vg1124874746 T -> DEL LOC_Os11g41470.1 N frameshift_variant Average:48.391; most accessible tissue: Minghui63 young leaf, score: 65.92 N N N N
vg1124874746 T -> C LOC_Os11g41470.1 missense_variant ; p.Thr526Ala; MODERATE nonsynonymous_codon ; T526A Average:48.391; most accessible tissue: Minghui63 young leaf, score: 65.92 benign -0.781 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124874746 NA 1.21E-11 mr1650 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
vg1124874746 NA 3.37E-06 mr1657 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
vg1124874746 NA 1.21E-10 mr1959 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
vg1124874746 8.69E-07 8.68E-07 mr1036_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
vg1124874746 NA 2.99E-07 mr1042_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
vg1124874746 NA 3.18E-06 mr1153_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
vg1124874746 NA 2.99E-32 mr1310_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
vg1124874746 NA 9.85E-08 mr1310_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
vg1124874746 NA 6.21E-07 mr1347_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
vg1124874746 NA 2.76E-06 mr1398_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
vg1124874746 NA 3.12E-09 mr1543_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
vg1124874746 NA 1.95E-08 mr1582_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
vg1124874746 NA 2.43E-09 mr1742_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
vg1124874746 NA 4.87E-09 mr1871_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
vg1124874746 NA 1.08E-15 mr1959_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
vg1124874746 NA 3.12E-06 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
vg1124874746 NA 5.74E-07 mr1966_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