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Detailed information for vg0812659243:

Variant ID: vg0812659243 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 12659243
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTCGATATGCATTCCCTCTACTGTAGGAAGCGGCTGGACGCCAATTTGATTGCCATCTGGTGTCTGTAAGTGCTACACTTGAACGTGTTAATAGATCA[T/C]
TACACCTATATGCGTAGCTCATTTGATCATCCATTGTGGCAGGATGAATTACGTGGAAGCCGAAGCGATGAAAAAGCCTGTCGCCTACCTAAACCCGTGC

Reverse complement sequence

GCACGGGTTTAGGTAGGCGACAGGCTTTTTCATCGCTTCGGCTTCCACGTAATTCATCCTGCCACAATGGATGATCAAATGAGCTACGCATATAGGTGTA[A/G]
TGATCTATTAACACGTTCAAGTGTAGCACTTACAGACACCAGATGGCAATCAAATTGGCGTCCAGCCGCTTCCTACAGTAGAGGGAATGCATATCGAAGA

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 38.70% 1.20% 12.25% 47.84% NA
All Indica  2759 20.80% 2.00% 17.47% 59.70% NA
All Japonica  1512 68.40% 0.10% 2.91% 28.57% NA
Aus  269 60.20% 0.00% 10.04% 29.74% NA
Indica I  595 12.80% 0.80% 13.28% 73.11% NA
Indica II  465 18.70% 3.20% 16.99% 61.08% NA
Indica III  913 25.50% 1.40% 20.59% 52.46% NA
Indica Intermediate  786 22.80% 2.80% 17.30% 57.12% NA
Temperate Japonica  767 90.60% 0.00% 0.65% 8.74% NA
Tropical Japonica  504 43.70% 0.40% 6.55% 49.40% NA
Japonica Intermediate  241 49.40% 0.00% 2.49% 48.13% NA
VI/Aromatic  96 13.50% 1.00% 16.67% 68.75% NA
Intermediate  90 47.80% 1.10% 11.11% 40.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0812659243 T -> C LOC_Os08g21200.1 missense_variant ; p.Ile476Thr; MODERATE nonsynonymous_codon ; I476T Average:10.103; most accessible tissue: Callus, score: 42.328 unknown unknown TOLERATED 0.17
vg0812659243 T -> DEL LOC_Os08g21200.1 N frameshift_variant Average:10.103; most accessible tissue: Callus, score: 42.328 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0812659243 NA 1.76E-08 mr1045 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
vg0812659243 NA 3.60E-08 mr1053 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
vg0812659243 NA 1.78E-06 mr1238 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
vg0812659243 NA 9.63E-07 mr1309 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
vg0812659243 NA 1.24E-07 mr1599 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
vg0812659243 NA 2.65E-14 mr1746 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
vg0812659243 NA 7.15E-09 mr1746 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
vg0812659243 NA 3.26E-07 mr1763 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
vg0812659243 NA 1.43E-08 mr1841 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
vg0812659243 7.49E-06 7.49E-06 mr1883 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
vg0812659243 NA 9.32E-06 mr1509_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
vg0812659243 NA 1.87E-06 mr1841_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