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Detailed information for vg0720354191:

Variant ID: vg0720354191 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 20354191
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCGAAAAAAGAAGTTGCAACTTGTTGATATGAGTATTCTATTAATCCTATTAACCCCTGGGCCGGGATGTTACACCCTCACCCCGTTAAGAGAGATCGA[C/T]
GCCCCCGTCGATCAACCCCAGGCGTCCCCTCTTGGCCACGTCCGTGTGTCCAGTGCTAGCGCATGTGCCATACTGTGTGACCACTCCGGGTCCACACTAG

Reverse complement sequence

CTAGTGTGGACCCGGAGTGGTCACACAGTATGGCACATGCGCTAGCACTGGACACACGGACGTGGCCAAGAGGGGACGCCTGGGGTTGATCGACGGGGGC[G/A]
TCGATCTCTCTTAACGGGGTGAGGGTGTAACATCCCGGCCCAGGGGTTAATAGGATTAATAGAATACTCATATCAACAAGTTGCAACTTCTTTTTTCGGA

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 85.10% 11.40% 1.27% 2.20% NA
All Indica  2759 97.00% 2.90% 0.07% 0.00% NA
All Japonica  1512 60.30% 29.10% 3.84% 6.75% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 94.10% 5.90% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.70% 0.13% 0.00% NA
Temperate Japonica  767 85.50% 7.70% 6.78% 0.00% NA
Tropical Japonica  504 14.70% 64.90% 0.60% 19.84% NA
Japonica Intermediate  241 75.50% 22.40% 1.24% 0.83% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0720354191 C -> DEL N N silent_mutation Average:69.354; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0720354191 C -> T LOC_Os07g34040.1 downstream_gene_variant ; 4660.0bp to feature; MODIFIER silent_mutation Average:69.354; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0720354191 C -> T LOC_Os07g34050.1 downstream_gene_variant ; 2601.0bp to feature; MODIFIER silent_mutation Average:69.354; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0720354191 C -> T LOC_Os07g34060.1 downstream_gene_variant ; 381.0bp to feature; MODIFIER silent_mutation Average:69.354; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0720354191 C -> T LOC_Os07g34060-LOC_Os07g34070 intergenic_region ; MODIFIER silent_mutation Average:69.354; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0720354191 NA 2.10E-06 mr1248 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
vg0720354191 4.55E-06 NA mr1563 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
vg0720354191 NA 3.56E-09 mr1563 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
vg0720354191 NA 5.28E-10 mr1705_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