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Detailed information for vg1216282324:

Variant ID: vg1216282324 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16282324
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGAGTCCACAAGTGGGCCAATCAAAACTCGCTACCCCTCCCAGGGCCCGTGCTGGAACGGTGTGTGTGAAAATGTGAATTACCAGTGCAACAACGGTG[T/C]
GTGTAAAAATGTTATAAAGCACATAATCAGTATTCGGCAAACCCACATTATCGCCACAAACAACAATCTTATTCGTGAAACAGTCGACGGTACAAGCAAA

Reverse complement sequence

TTTGCTTGTACCGTCGACTGTTTCACGAATAAGATTGTTGTTTGTGGCGATAATGTGGGTTTGCCGAATACTGATTATGTGCTTTATAACATTTTTACAC[A/G]
CACCGTTGTTGCACTGGTAATTCACATTTTCACACACACCGTTCCAGCACGGGCCCTGGGAGGGGTAGCGAGTTTTGATTGGCCCACTTGTGGACTCCCA

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 48.80% 40.60% 0.19% 10.41% NA
All Indica  2759 73.80% 21.40% 0.18% 4.68% NA
All Japonica  1512 15.20% 71.10% 0.20% 13.49% NA
Aus  269 3.70% 40.10% 0.37% 55.76% NA
Indica I  595 87.10% 9.20% 0.17% 3.53% NA
Indica II  465 65.40% 24.50% 0.00% 10.11% NA
Indica III  913 71.70% 25.50% 0.11% 2.63% NA
Indica Intermediate  786 71.00% 23.90% 0.38% 4.71% NA
Temperate Japonica  767 2.20% 97.50% 0.00% 0.26% NA
Tropical Japonica  504 36.30% 25.80% 0.60% 37.30% NA
Japonica Intermediate  241 12.40% 81.70% 0.00% 5.81% NA
VI/Aromatic  96 6.20% 92.70% 0.00% 1.04% NA
Intermediate  90 30.00% 61.10% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216282324 T -> C LOC_Os12g27650.1 downstream_gene_variant ; 2443.0bp to feature; MODIFIER silent_mutation Average:30.253; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N
vg1216282324 T -> C LOC_Os12g27650-LOC_Os12g27670 intergenic_region ; MODIFIER silent_mutation Average:30.253; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N
vg1216282324 T -> DEL N N silent_mutation Average:30.253; most accessible tissue: Zhenshan97 flag leaf, score: 69.147 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216282324 NA 8.13E-06 mr1106 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
vg1216282324 2.54E-06 1.46E-07 mr1268 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
vg1216282324 NA 1.53E-06 mr1304 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
vg1216282324 NA 7.43E-08 mr1364 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
vg1216282324 NA 8.46E-06 mr1364 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
vg1216282324 NA 2.29E-07 mr1443 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
vg1216282324 5.34E-06 NA mr1485 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
vg1216282324 NA 2.65E-06 mr1622 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
vg1216282324 NA 9.81E-06 mr1884 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
vg1216282324 NA 6.34E-07 mr1047_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
vg1216282324 NA 3.22E-06 mr1227_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
vg1216282324 NA 2.13E-06 mr1815_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