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Detailed information for vg0412333059:

Variant ID: vg0412333059 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12333059
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAAAAAAGAGCTTGGGACCCAACAGCGGCTGGTGGCACCCTAAAAAACGATTTTTCTATATAAGAGCTCCTCAATAGGTTGCGGACAGATTGTAAGTG[T/C]
TCATGTCTGTAAAAATCGATCCCCTATTTTCGCATATGGCCCATATGTAAAAATCTATTTTCGTAGATGACACTCTTAAGAAGCCACATGGGAAAATAGG

Reverse complement sequence

CCTATTTTCCCATGTGGCTTCTTAAGAGTGTCATCTACGAAAATAGATTTTTACATATGGGCCATATGCGAAAATAGGGGATCGATTTTTACAGACATGA[A/G]
CACTTACAATCTGTCCGCAACCTATTGAGGAGCTCTTATATAGAAAAATCGTTTTTTAGGGTGCCACCAGCCGCTGTTGGGTCCCAAGCTCTTTTTTTTT

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 91.20% 4.10% 4.63% 0.00% NA
All Indica  2759 99.70% 0.10% 0.14% 0.00% NA
All Japonica  1512 73.70% 12.30% 13.96% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.40% 0.20% 0.43% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 53.20% 22.70% 24.12% 0.00% NA
Tropical Japonica  504 96.80% 0.60% 2.58% 0.00% NA
Japonica Intermediate  241 90.90% 3.70% 5.39% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 90.00% 7.80% 2.22% 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
vg0412333059 T -> C LOC_Os04g21780-LOC_Os04g21790 intergenic_region ; MODIFIER silent_mutation Average:41.393; most accessible tissue: Callus, score: 54.604 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412333059 NA 5.26E-07 mr1002 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
vg0412333059 NA 3.42E-07 mr1182 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
vg0412333059 NA 4.90E-06 mr1282 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
vg0412333059 8.97E-06 8.97E-06 mr1465 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
vg0412333059 NA 9.86E-07 mr1650 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
vg0412333059 NA 9.20E-08 mr1748_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