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Detailed information for vg0107150999:

Variant ID: vg0107150999 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7150999
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGTCCTCTATTTTGTAAAACCACTCACACTAGACGCACTATTTTTTTTTAACAAGATGTATGTGCTGTGTATAAAAAAATCCTACTAGCTGGCCCACT[A/C]
TTTTGCAAAATGTACTGCAAATACTGATCGAGAACTTCAGTTGTCAAAAGAAGGACCTATACTATGCATGTTTTGCATGATAAGATAAAGCACGAAACGC

Reverse complement sequence

GCGTTTCGTGCTTTATCTTATCATGCAAAACATGCATAGTATAGGTCCTTCTTTTGACAACTGAAGTTCTCGATCAGTATTTGCAGTACATTTTGCAAAA[T/G]
AGTGGGCCAGCTAGTAGGATTTTTTTATACACAGCACATACATCTTGTTAAAAAAAAATAGTGCGTCTAGTGTGAGTGGTTTTACAAAATAGAGGACATG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.70% 16.90% 0.00% 0.36% NA
All Indica  2759 71.10% 28.30% 0.00% 0.62% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 91.80% 7.90% 0.00% 0.34% NA
Indica II  465 65.80% 34.00% 0.00% 0.22% NA
Indica III  913 67.40% 31.80% 0.00% 0.88% NA
Indica Intermediate  786 63.00% 36.30% 0.00% 0.76% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 0.00% 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
vg0107150999 A -> DEL N N silent_mutation Average:34.969; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N
vg0107150999 A -> C LOC_Os01g12880-LOC_Os01g12890 intergenic_region ; MODIFIER silent_mutation Average:34.969; most accessible tissue: Zhenshan97 panicle, score: 49.416 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107150999 NA 5.15E-08 mr1498 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
vg0107150999 2.56E-06 NA mr1699 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
vg0107150999 7.37E-06 2.57E-07 mr1699 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
vg0107150999 NA 2.11E-07 mr1925 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
vg0107150999 NA 9.22E-09 mr1951 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
vg0107150999 NA 4.37E-06 mr1160_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
vg0107150999 NA 7.65E-06 mr1160_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
vg0107150999 NA 2.55E-09 mr1498_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
vg0107150999 1.09E-08 NA mr1699_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
vg0107150999 2.10E-07 2.54E-12 mr1699_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
vg0107150999 3.16E-06 NA mr1745_2 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