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Detailed information for vg0612586290:

Variant ID: vg0612586290 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 12586290
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.06, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


CGGAGATCGATGATGAAGAGATGGCTCTCTTCGTCAAGAAGTTCGGCAAGTTCATGAAGCAAAGCGGCTTCTTTAAGGGAAGTTCGTCCAAGTATTCCTC[T/C]
AACAAGTCAAGTGGAAGACACTCCGCAAGGGTGTGCTATGTGTGCAAAGAGCCCGGGCACTTCATTGCGGATTGCCCTCACATCAAGGATTGCCCCCACT

Reverse complement sequence

AGTGGGGGCAATCCTTGATGTGAGGGCAATCCGCAATGAAGTGCCCGGGCTCTTTGCACACATAGCACACCCTTGCGGAGTGTCTTCCACTTGACTTGTT[A/G]
GAGGAATACTTGGACGAACTTCCCTTAAAGAAGCCGCTTTGCTTCATGAACTTGCCGAACTTCTTGACGAAGAGAGCCATCTCTTCATCATCGATCTCCG

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 37.90% 0.90% 14.98% 46.23% NA
All Indica  2759 10.30% 1.40% 23.99% 64.26% NA
All Japonica  1512 89.40% 0.20% 1.06% 9.39% NA
Aus  269 17.50% 0.00% 6.69% 75.84% NA
Indica I  595 17.30% 0.50% 5.71% 76.47% NA
Indica II  465 10.10% 3.20% 30.97% 55.70% NA
Indica III  913 3.10% 0.90% 32.53% 63.53% NA
Indica Intermediate  786 13.50% 1.80% 23.79% 60.94% NA
Temperate Japonica  767 97.10% 0.00% 0.91% 1.96% NA
Tropical Japonica  504 76.80% 0.60% 0.99% 21.63% NA
Japonica Intermediate  241 90.90% 0.00% 1.66% 7.47% NA
VI/Aromatic  96 61.50% 0.00% 0.00% 38.54% NA
Intermediate  90 54.40% 0.00% 13.33% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0612586290 T -> C LOC_Os06g21780.1 synonymous_variant ; p.Ser257Ser; LOW synonymous_codon Average:9.746; most accessible tissue: Callus, score: 31.401 N N N N
vg0612586290 T -> DEL LOC_Os06g21780.1 N frameshift_variant Average:9.746; most accessible tissue: Callus, score: 31.401 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0612586290 NA 1.58E-28 mr1075 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
vg0612586290 5.84E-06 NA mr1078 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
vg0612586290 NA 8.17E-08 mr1082 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
vg0612586290 NA 6.69E-06 mr1103 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
vg0612586290 NA 2.13E-06 mr1104 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
vg0612586290 NA 1.09E-06 mr1107 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
vg0612586290 NA 3.20E-06 mr1145 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
vg0612586290 NA 7.73E-06 mr1155 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
vg0612586290 NA 7.08E-31 mr1202 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
vg0612586290 NA 7.95E-08 mr1226 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
vg0612586290 4.82E-07 NA mr1234 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
vg0612586290 1.82E-07 NA mr1234 Ind_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
vg0612586290 NA 1.20E-07 mr1411 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
vg0612586290 NA 2.98E-06 mr1518 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
vg0612586290 NA 5.44E-39 mr1534 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
vg0612586290 NA 3.60E-06 mr1534 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
vg0612586290 NA 1.18E-19 mr1541 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
vg0612586290 1.09E-06 6.30E-09 mr1560 Ind_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
vg0612586290 NA 4.84E-21 mr1588 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
vg0612586290 NA 6.35E-11 mr1713 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