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Detailed information for vg0432523918:

Variant ID: vg0432523918 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32523918
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.68, T: 0.32, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


GCGCTCGCTCCTCCAGCTCCTGGGCCCGCCCCGTCTGTTCTTCGCCGCACGTTTTTTGCTCGCGCTGGTTTCGATCGAGGACTTCGATCCACCGACGGAT[T/C]
GTGGCTTCAAGCTCCTGTGCGGAGCGAGCACGGTCATCCAAGGCCTTGCGCTCAGCCCCGAGCGCCGTCGTTCGAGCCTGCAGAGAGGCCTCAGCCTCCG

Reverse complement sequence

CGGAGGCTGAGGCCTCTCTGCAGGCTCGAACGACGGCGCTCGGGGCTGAGCGCAAGGCCTTGGATGACCGTGCTCGCTCCGCACAGGAGCTTGAAGCCAC[A/G]
ATCCGTCGGTGGATCGAAGTCCTCGATCGAAACCAGCGCGAGCAAAAAACGTGCGGCGAAGAACAGACGGGGCGGGCCCAGGAGCTGGAGGAGCGAGCGC

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 66.70% 32.80% 0.40% 0.13% NA
All Indica  2759 73.10% 26.40% 0.33% 0.22% NA
All Japonica  1512 64.50% 35.00% 0.53% 0.00% NA
Aus  269 14.90% 85.10% 0.00% 0.00% NA
Indica I  595 91.80% 8.20% 0.00% 0.00% NA
Indica II  465 74.00% 25.80% 0.22% 0.00% NA
Indica III  913 56.60% 42.30% 0.66% 0.44% NA
Indica Intermediate  786 77.50% 22.00% 0.25% 0.25% NA
Temperate Japonica  767 72.80% 26.30% 0.91% 0.00% NA
Tropical Japonica  504 67.30% 32.70% 0.00% 0.00% NA
Japonica Intermediate  241 32.40% 67.20% 0.41% 0.00% NA
VI/Aromatic  96 63.50% 34.40% 2.08% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg0432523918 T -> C LOC_Os04g54670.1 synonymous_variant ; p.Thr1459Thr; LOW synonymous_codon Average:70.549; most accessible tissue: Minghui63 young leaf, score: 84.596 N N N N
vg0432523918 T -> DEL LOC_Os04g54670.1 N frameshift_variant Average:70.549; most accessible tissue: Minghui63 young leaf, score: 84.596 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432523918 NA 4.36E-06 mr1403 Ind_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
vg0432523918 9.12E-08 9.46E-11 mr1800 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
vg0432523918 2.85E-07 5.41E-09 mr1800 Ind_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
vg0432523918 NA 2.13E-06 mr1638_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
vg0432523918 NA 9.82E-06 mr1729_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
vg0432523918 1.20E-06 1.14E-09 mr1740_2 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
vg0432523918 6.36E-09 4.81E-12 mr1741_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
vg0432523918 2.11E-08 NA mr1771_2 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
vg0432523918 4.62E-07 NA mr1771_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
vg0432523918 3.94E-09 NA mr1784_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
vg0432523918 3.61E-08 6.67E-08 mr1785_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
vg0432523918 4.86E-06 1.51E-06 mr1786_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
vg0432523918 3.77E-16 1.22E-19 mr1800_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
vg0432523918 1.69E-11 2.48E-12 mr1800_2 Ind_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
vg0432523918 2.56E-07 NA mr1873_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