\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0905711051:

Variant ID: vg0905711051 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5711051
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATATGCCGATTCGTGAGCTTCCTTTAGGATTAATCCTCTCAGTCCACCCTGTTCGGGTACATAGATCCTCTTTTTATACCAAAGGACATCTTTTTCATC[G/T]
GTCAAAAATTCCTTTGCAAACCCTGCAGCTAGGCGTTCCTTCACCTCTTGGATTTCTTCGTTGTCCTTCTGGGCTTCTTCTATTTGGGTTCTCAAAAGAG

Reverse complement sequence

CTCTTTTGAGAACCCAAATAGAAGAAGCCCAGAAGGACAACGAAGAAATCCAAGAGGTGAAGGAACGCCTAGCTGCAGGGTTTGCAAAGGAATTTTTGAC[C/A]
GATGAAAAAGATGTCCTTTGGTATAAAAAGAGGATCTATGTACCCGAACAGGGTGGACTGAGAGGATTAATCCTAAAGGAAGCTCACGAATCGGCATATT

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 60.30% 32.50% 1.04% 6.16% NA
All Indica  2759 91.10% 8.20% 0.65% 0.00% NA
All Japonica  1512 1.90% 81.40% 0.26% 16.47% NA
Aus  269 87.40% 11.90% 0.74% 0.00% NA
Indica I  595 80.70% 17.60% 1.68% 0.00% NA
Indica II  465 90.10% 9.50% 0.43% 0.00% NA
Indica III  913 97.00% 2.80% 0.11% 0.00% NA
Indica Intermediate  786 92.70% 6.60% 0.64% 0.00% NA
Temperate Japonica  767 1.30% 90.70% 0.39% 7.56% NA
Tropical Japonica  504 1.40% 82.10% 0.00% 16.47% NA
Japonica Intermediate  241 4.60% 50.20% 0.41% 44.81% NA
VI/Aromatic  96 31.20% 3.10% 25.00% 40.62% NA
Intermediate  90 46.70% 48.90% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0905711051 G -> DEL LOC_Os09g10450.1 N frameshift_variant Average:27.524; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0905711051 G -> T LOC_Os09g10450.1 synonymous_variant ; p.Thr502Thr; LOW synonymous_codon Average:27.524; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905711051 NA 2.57E-07 mr1162 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
vg0905711051 NA 4.14E-10 mr1191 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
vg0905711051 7.94E-06 NA mr1547 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
vg0905711051 7.57E-06 2.10E-11 mr1637 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
vg0905711051 NA 4.96E-07 mr1785 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
vg0905711051 NA 1.44E-07 mr1804 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
vg0905711051 NA 7.67E-11 mr1905 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
vg0905711051 2.78E-06 NA mr1937 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
vg0905711051 NA 1.78E-20 mr1010_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
vg0905711051 NA 3.47E-14 mr1191_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
vg0905711051 NA 5.57E-07 mr1212_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
vg0905711051 NA 3.33E-12 mr1216_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