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Detailed information for vg0119842659:

Variant ID: vg0119842659 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 19842659
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATGCATTTGGTACCGGCCCACGAGGAACCCCGATACTCGCTTGCGGCAAAGGATGATTACTGTATGTGGATTGAAAATATGGATGCTGTAAATTAGAA[T/C]
TAAAACCAACACTACAGCTGTTGCTATTAAGGTTTTGTGGACTTAACACTGGAATAATAGAATTAGTAGTGCTAGTTGAAACACTAGGTACAGAACTACC

Reverse complement sequence

GGTAGTTCTGTACCTAGTGTTTCAACTAGCACTACTAATTCTATTATTCCAGTGTTAAGTCCACAAAACCTTAATAGCAACAGCTGTAGTGTTGGTTTTA[A/G]
TTCTAATTTACAGCATCCATATTTTCAATCCACATACAGTAATCATCCTTTGCCGCAAGCGAGTATCGGGGTTCCTCGTGGGCCGGTACCAAATGCATGT

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 70.30% 11.90% 1.97% 15.85% NA
All Indica  2759 52.70% 19.90% 2.94% 24.47% NA
All Japonica  1512 98.20% 0.70% 0.07% 0.99% NA
Aus  269 77.30% 0.40% 3.72% 18.59% NA
Indica I  595 59.30% 16.80% 2.35% 21.51% NA
Indica II  465 73.30% 1.30% 1.94% 23.44% NA
Indica III  913 34.30% 35.00% 3.07% 27.60% NA
Indica Intermediate  786 56.90% 15.60% 3.82% 23.66% NA
Temperate Japonica  767 98.70% 1.20% 0.00% 0.13% NA
Tropical Japonica  504 98.60% 0.20% 0.00% 1.19% NA
Japonica Intermediate  241 95.90% 0.40% 0.41% 3.32% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 87.80% 2.20% 1.11% 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
vg0119842659 T -> DEL N N silent_mutation Average:29.992; most accessible tissue: Minghui63 flag leaf, score: 74.955 N N N N
vg0119842659 T -> C LOC_Os01g35830.1 downstream_gene_variant ; 2989.0bp to feature; MODIFIER silent_mutation Average:29.992; most accessible tissue: Minghui63 flag leaf, score: 74.955 N N N N
vg0119842659 T -> C LOC_Os01g35820.1 intron_variant ; MODIFIER silent_mutation Average:29.992; most accessible tissue: Minghui63 flag leaf, score: 74.955 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0119842659 NA 9.38E-10 mr1707 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
vg0119842659 NA 4.75E-06 mr1707 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
vg0119842659 3.49E-06 5.35E-12 mr1728 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
vg0119842659 NA 1.52E-07 mr1728 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
vg0119842659 NA 5.05E-10 mr1860 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
vg0119842659 NA 1.32E-06 mr1860 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
vg0119842659 NA 7.08E-06 mr1825_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