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Detailed information for vg0907785140:

Variant ID: vg0907785140 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 7785140
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCTGTAGAAAAAAGTTTGACTAATTCTGTAGAAAAAACTAGTCAGCATAATTTCATTAAATCTATAATTGAATAAGTTTTCATAATATATTTGTCTTGG[T/C]
TAAAAATATTACTATTTTTTTTATAAAATTAGTCAAAGTTAGAGTAGTTTAACTTTGATCAATGTCAAAATATCTTATAAGCTAAAACGGAGGTAGTAGC

Reverse complement sequence

GCTACTACCTCCGTTTTAGCTTATAAGATATTTTGACATTGATCAAAGTTAAACTACTCTAACTTTGACTAATTTTATAAAAAAAATAGTAATATTTTTA[A/G]
CCAAGACAAATATATTATGAAAACTTATTCAATTATAGATTTAATGAAATTATGCTGACTAGTTTTTTCTACAGAATTAGTCAAACTTTTTTCTACAGAA

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 97.30% 0.50% 0.47% 1.80% NA
All Indica  2759 99.80% 0.00% 0.00% 0.18% NA
All Japonica  1512 93.20% 1.40% 1.46% 3.97% NA
Aus  269 92.90% 0.00% 0.00% 7.06% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.10% 0.00% 0.64% NA
Temperate Japonica  767 89.60% 2.70% 2.61% 5.08% NA
Tropical Japonica  504 96.00% 0.00% 0.00% 3.97% NA
Japonica Intermediate  241 98.80% 0.00% 0.83% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0907785140 T -> DEL N N silent_mutation Average:41.232; most accessible tissue: Zhenshan97 root, score: 68.908 N N N N
vg0907785140 T -> C LOC_Os09g13460.1 upstream_gene_variant ; 2826.0bp to feature; MODIFIER silent_mutation Average:41.232; most accessible tissue: Zhenshan97 root, score: 68.908 N N N N
vg0907785140 T -> C LOC_Os09g13460-LOC_Os09g13470 intergenic_region ; MODIFIER silent_mutation Average:41.232; most accessible tissue: Zhenshan97 root, score: 68.908 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0907785140 1.39E-06 1.24E-10 mr1062 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
vg0907785140 6.61E-06 1.47E-06 mr1677 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
vg0907785140 3.74E-06 3.74E-06 mr1950 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
vg0907785140 NA 8.05E-06 mr1932_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