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Detailed information for vg0622948498:

Variant ID: vg0622948498 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 22948498
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCAAAAGGTTGCCAACGTTAGGTATTCGAAAATGCCACAAATTAAGATGTGTTCACATCTTAGTATCCCACGGGGTCCTCTTCGGTCGTCTCGATTGGT[T/C]
AATTAAAATTCTGTCCTCGTCTGGCATACAAATCCTGCCAAATTTCTTGGTTAGATTGTCATATCAAGCTCAGGACAATGTGTTTTGTTTTCATTTGGTG

Reverse complement sequence

CACCAAATGAAAACAAAACACATTGTCCTGAGCTTGATATGACAATCTAACCAAGAAATTTGGCAGGATTTGTATGCCAGACGAGGACAGAATTTTAATT[A/G]
ACCAATCGAGACGACCGAAGAGGACCCCGTGGGATACTAAGATGTGAACACATCTTAATTTGTGGCATTTTCGAATACCTAACGTTGGCAACCTTTTGAC

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 26.80% 5.10% 0.89% 67.29% NA
All Indica  2759 5.00% 0.20% 1.27% 93.48% NA
All Japonica  1512 68.00% 14.80% 0.20% 17.00% NA
Aus  269 5.20% 1.50% 1.12% 92.19% NA
Indica I  595 1.30% 0.20% 1.68% 96.81% NA
Indica II  465 8.00% 0.00% 1.29% 90.75% NA
Indica III  913 4.70% 0.00% 0.55% 94.74% NA
Indica Intermediate  786 6.50% 0.60% 1.78% 91.09% NA
Temperate Japonica  767 53.60% 27.20% 0.26% 18.90% NA
Tropical Japonica  504 86.90% 1.40% 0.20% 11.51% NA
Japonica Intermediate  241 74.30% 3.30% 0.00% 22.41% NA
VI/Aromatic  96 45.80% 1.00% 0.00% 53.12% NA
Intermediate  90 44.40% 4.40% 1.11% 50.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0622948498 T -> C LOC_Os06g38650.1 upstream_gene_variant ; 2898.0bp to feature; MODIFIER silent_mutation Average:12.11; most accessible tissue: Callus, score: 76.947 N N N N
vg0622948498 T -> C LOC_Os06g38640-LOC_Os06g38650 intergenic_region ; MODIFIER silent_mutation Average:12.11; most accessible tissue: Callus, score: 76.947 N N N N
vg0622948498 T -> DEL N N silent_mutation Average:12.11; most accessible tissue: Callus, score: 76.947 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0622948498 NA 3.94E-06 mr1305 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
vg0622948498 3.35E-07 NA mr1585 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
vg0622948498 NA 3.31E-09 mr1585 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
vg0622948498 2.12E-06 NA mr1586 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
vg0622948498 NA 1.05E-06 mr1586 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
vg0622948498 NA 1.67E-06 mr1765 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
vg0622948498 NA 5.85E-08 mr1915 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
vg0622948498 7.61E-07 7.61E-07 mr1571_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