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Detailed information for vg1208212616:

Variant ID: vg1208212616 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8212616
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGTGGATTACCAGGGCAAGCAGCTCCCGGAGCAGGAGGGTGACGATGTAGAGCCCCATGCTGCTTGGGAGGTCACTGCAGTGATCCTCACTGGCTCACC[T/C]
GAGAGGACTTCGTTGGCAGTCACCGCGGGAGGAGATTCTTTCTCTGCCGCTTGCCAGAACGCCGCACTCCTCGCCATCGGCACTCTTCACCAGCGCTACC

Reverse complement sequence

GGTAGCGCTGGTGAAGAGTGCCGATGGCGAGGAGTGCGGCGTTCTGGCAAGCGGCAGAGAAAGAATCTCCTCCCGCGGTGACTGCCAACGAAGTCCTCTC[A/G]
GGTGAGCCAGTGAGGATCACTGCAGTGACCTCCCAAGCAGCATGGGGCTCTACATCGTCACCCTCCTGCTCCGGGAGCTGCTTGCCCTGGTAATCCACTC

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 57.30% 1.30% 12.46% 28.93% NA
All Indica  2759 55.90% 1.40% 8.74% 33.96% NA
All Japonica  1512 53.50% 1.40% 18.52% 26.59% NA
Aus  269 85.50% 0.40% 13.38% 0.74% NA
Indica I  595 51.10% 0.20% 4.37% 44.37% NA
Indica II  465 45.20% 0.40% 9.68% 44.73% NA
Indica III  913 65.30% 2.50% 12.16% 20.04% NA
Indica Intermediate  786 55.00% 1.70% 7.51% 35.88% NA
Temperate Japonica  767 76.00% 0.00% 4.95% 19.04% NA
Tropical Japonica  504 25.00% 3.40% 39.88% 31.75% NA
Japonica Intermediate  241 41.50% 1.70% 17.01% 39.83% NA
VI/Aromatic  96 69.80% 1.00% 19.79% 9.38% NA
Intermediate  90 65.60% 1.10% 14.44% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208212616 T -> C LOC_Os12g14400.1 synonymous_variant ; p.Pro134Pro; LOW synonymous_codon Average:29.84; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg1208212616 T -> DEL LOC_Os12g14400.1 N frameshift_variant Average:29.84; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208212616 5.88E-06 2.62E-08 mr1083 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
vg1208212616 NA 5.77E-06 mr1226 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
vg1208212616 5.01E-09 5.01E-09 mr1076_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
vg1208212616 NA 2.58E-08 mr1083_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
vg1208212616 NA 9.14E-06 mr1103_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
vg1208212616 NA 9.87E-06 mr1104_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
vg1208212616 NA 4.13E-06 mr1107_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
vg1208212616 NA 5.25E-08 mr1226_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
vg1208212616 NA 6.38E-07 mr1408_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