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Detailed information for vg0625951448:

Variant ID: vg0625951448 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25951448
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAAGAAACATCATTGATATATACTTCCTCCGTTTCGAAATGTTTGACACCGTTGACTTTTTAACACATGTTTGACCGTTCGTCTTATTCAAAAACTTT[T/G]
ATGAAATATGTAAAATTATATGCCTACATAAAAATATATTTAACAATAAATCAAATGATAGAAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGAC

Reverse complement sequence

GTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTTCTATCATTTGATTTATTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATTTCAT[A/C]
AAAGTTTTTGAATAAGACGAACGGTCAAACATGTGTTAAAAAGTCAACGGTGTCAAACATTTCGAAACGGAGGAAGTATATATCAATGATGTTTCTTAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.40% 3.60% 2.52% 61.49% NA
All Indica  2759 3.90% 0.00% 0.65% 95.40% NA
All Japonica  1512 86.00% 11.30% 1.46% 1.26% NA
Aus  269 5.60% 0.00% 25.65% 68.77% NA
Indica I  595 1.70% 0.00% 0.50% 97.82% NA
Indica II  465 6.90% 0.20% 0.00% 92.90% NA
Indica III  913 1.00% 0.00% 0.33% 98.69% NA
Indica Intermediate  786 7.30% 0.00% 1.53% 91.22% NA
Temperate Japonica  767 78.50% 20.20% 0.13% 1.17% NA
Tropical Japonica  504 94.00% 0.20% 3.77% 1.98% NA
Japonica Intermediate  241 92.90% 6.20% 0.83% 0.00% NA
VI/Aromatic  96 64.60% 0.00% 4.17% 31.25% NA
Intermediate  90 48.90% 0.00% 6.67% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0625951448 T -> G LOC_Os06g43170.1 upstream_gene_variant ; 1903.0bp to feature; MODIFIER silent_mutation Average:55.253; most accessible tissue: Zhenshan97 root, score: 86.685 N N N N
vg0625951448 T -> G LOC_Os06g43170-LOC_Os06g43180 intergenic_region ; MODIFIER silent_mutation Average:55.253; most accessible tissue: Zhenshan97 root, score: 86.685 N N N N
vg0625951448 T -> DEL N N silent_mutation Average:55.253; most accessible tissue: Zhenshan97 root, score: 86.685 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625951448 NA 2.26E-06 mr1006 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
vg0625951448 NA 7.20E-06 mr1052 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
vg0625951448 NA 6.19E-07 mr1210 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
vg0625951448 NA 2.10E-06 mr1280 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
vg0625951448 NA 7.42E-07 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
vg0625951448 2.03E-06 2.03E-06 mr1370 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
vg0625951448 NA 7.92E-06 mr1515 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
vg0625951448 NA 6.60E-07 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
vg0625951448 NA 1.40E-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
vg0625951448 NA 5.52E-07 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
vg0625951448 NA 6.67E-07 mr1788 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
vg0625951448 7.14E-07 1.62E-10 mr1305_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
vg0625951448 2.86E-06 2.86E-06 mr1317_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
vg0625951448 NA 9.67E-06 mr1559_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
vg0625951448 NA 7.62E-11 mr1585_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
vg0625951448 NA 6.91E-06 mr1765_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