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Detailed information for vg0620514657:

Variant ID: vg0620514657 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20514657
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGCAGAAGTCAGGAAGCTGGAAAAAAAGGTTTGATAGGATCGAGGTCCGACATGTATACCCCAAAGACAACATCGAACCGGATGATCTAGCACGGCGTG[T/C]
GTCCAGACGAGAGCCACTTGAACCTGGCACCTTTCTGGACGTCTTGACCAGACCATTAGTGAAAGAGGCAAGCGGCGAAGATAGCCCGGTCACCCACAAC

Reverse complement sequence

GTTGTGGGTGACCGGGCTATCTTCGCCGCTTGCCTCTTTCACTAATGGTCTGGTCAAGACGTCCAGAAAGGTGCCAGGTTCAAGTGGCTCTCGTCTGGAC[A/G]
CACGCCGTGCTAGATCATCCGGTTCGATGTTGTCTTTGGGGTATACATGTCGGACCTCGATCCTATCAAACCTTTTTTTCCAGCTTCCTGACTTCTGCGA

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 51.20% 2.10% 22.83% 23.91% NA
All Indica  2759 37.60% 0.30% 28.49% 33.64% NA
All Japonica  1512 85.80% 4.80% 1.92% 7.41% NA
Aus  269 3.70% 0.70% 77.32% 18.22% NA
Indica I  595 29.60% 0.00% 29.41% 41.01% NA
Indica II  465 45.40% 0.60% 25.81% 28.17% NA
Indica III  913 37.30% 0.40% 28.70% 33.52% NA
Indica Intermediate  786 39.40% 0.00% 29.13% 31.42% NA
Temperate Japonica  767 91.50% 5.10% 0.52% 2.87% NA
Tropical Japonica  504 91.50% 1.00% 3.97% 3.57% NA
Japonica Intermediate  241 56.00% 12.00% 2.07% 29.88% NA
VI/Aromatic  96 17.70% 13.50% 42.71% 26.04% NA
Intermediate  90 61.10% 4.40% 16.67% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620514657 T -> C LOC_Os06g35190.1 downstream_gene_variant ; 2002.0bp to feature; MODIFIER silent_mutation Average:8.618; most accessible tissue: Callus, score: 19.455 N N N N
vg0620514657 T -> C LOC_Os06g35180.1 intron_variant ; MODIFIER silent_mutation Average:8.618; most accessible tissue: Callus, score: 19.455 N N N N
vg0620514657 T -> DEL N N silent_mutation Average:8.618; most accessible tissue: Callus, score: 19.455 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620514657 6.28E-06 1.68E-06 mr1415 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
vg0620514657 6.28E-06 1.68E-06 mr1567 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
vg0620514657 1.84E-06 4.81E-07 mr1037_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
vg0620514657 3.93E-06 3.93E-06 mr1168_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
vg0620514657 2.33E-07 2.33E-07 mr1367_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
vg0620514657 NA 9.01E-06 mr1565_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
vg0620514657 NA 7.73E-07 mr1567_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
vg0620514657 NA 9.10E-06 mr1567_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
vg0620514657 NA 8.42E-06 mr1591_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
vg0620514657 NA 3.95E-06 mr1726_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
vg0620514657 1.34E-06 1.34E-06 mr1806_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
vg0620514657 NA 7.96E-08 mr1827_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