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Detailed information for vg1125474766:

Variant ID: vg1125474766 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25474766
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGCACCTTGGCGTTGGTGAAGTTGTGGATGAAATGCGAGTAGTCGACGCATCGCCCCATGCCATGGGTGAAGTGGAGGTCGGCGGCGACCACCGTCGTC[G/C]
TGTCCGGCGACGGCGGCGAGGTTAGGTCGAACAGCACCGCTTCTCCCTTGTACGTGAAGGATCGCAGCCTCAGCGCGGTGATCTCCATTGATCTGCCCGG

Reverse complement sequence

CCGGGCAGATCAATGGAGATCACCGCGCTGAGGCTGCGATCCTTCACGTACAAGGGAGAAGCGGTGCTGTTCGACCTAACCTCGCCGCCGTCGCCGGACA[C/G]
GACGACGGTGGTCGCCGCCGACCTCCACTTCACCCATGGCATGGGGCGATGCGTCGACTACTCGCATTTCATCCACAACTTCACCAACGCCAAGGTGCTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 2.90% 0.28% 0.00% NA
All Indica  2759 99.00% 0.90% 0.04% 0.00% NA
All Japonica  1512 99.00% 1.00% 0.00% 0.00% NA
Aus  269 79.60% 16.40% 4.09% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 47.90% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg1125474766 G -> C LOC_Os11g42300.1 missense_variant ; p.Thr289Arg; MODERATE nonsynonymous_codon ; T289R Average:72.081; most accessible tissue: Minghui63 panicle, score: 82.128 unknown unknown TOLERATED 0.54

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125474766 4.86E-09 NA mr1191 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
vg1125474766 2.08E-08 7.91E-10 mr1644 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
vg1125474766 2.18E-11 NA mr1191_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
vg1125474766 NA 2.41E-06 mr1465_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
vg1125474766 NA 5.43E-06 mr1522_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
vg1125474766 NA 2.76E-08 mr1567_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
vg1125474766 3.45E-07 2.62E-11 mr1662_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