Search for Variation information by Variation ID:

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

Detailed information for vg0920821502:

Variant ID: vg0920821502 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20821502
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTGATTCGGCCACGTGTTACATTGCTGACTTCAAACGGCCGCCAAATCTACATACGTGCTCCGTTTTGGGCCCGTGAGTACTTGATGGAAAGCTCTCG[A/G]
AGTCCTCCTTCCAACGGATCCAGCCTCATCTCGAAATTCTATCTCGTTTGGCCGCAAGGTGCTGCGTCACCTGTATTGGGCCAATGGGCTTGTAACTTTG

Reverse complement sequence

CAAAGTTACAAGCCCATTGGCCCAATACAGGTGACGCAGCACCTTGCGGCCAAACGAGATAGAATTTCGAGATGAGGCTGGATCCGTTGGAAGGAGGACT[T/C]
CGAGAGCTTTCCATCAAGTACTCACGGGCCCAAAACGGAGCACGTATGTAGATTTGGCGGCCGTTTGAAGTCAGCAATGTAACACGTGGCCGAATCAGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 48.90% 42.50% 1.04% 7.64% NA
All Indica  2759 82.70% 11.30% 1.01% 4.89% NA
All Japonica  1512 0.10% 99.40% 0.13% 0.33% NA
Aus  269 1.50% 13.80% 6.69% 78.07% NA
Indica I  595 86.90% 9.40% 1.18% 2.52% NA
Indica II  465 84.10% 7.50% 0.65% 7.74% NA
Indica III  913 84.60% 11.60% 0.66% 3.18% NA
Indica Intermediate  786 76.70% 14.80% 1.53% 7.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 96.70% 0.83% 2.07% NA
VI/Aromatic  96 0.00% 95.80% 0.00% 4.17% NA
Intermediate  90 22.20% 68.90% 1.11% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0920821502 A -> G LOC_Os09g36140-LOC_Os09g36150 intergenic_region ; MODIFIER silent_mutation Average:38.044; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg0920821502 A -> DEL N N silent_mutation Average:38.044; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920821502 NA 1.56E-06 mr1029 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
vg0920821502 NA 2.56E-10 mr1047 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
vg0920821502 NA 5.29E-08 mr1189 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
vg0920821502 NA 5.53E-07 mr1625 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
vg0920821502 NA 5.15E-08 mr1796 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
vg0920821502 NA 8.91E-09 mr1990 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
vg0920821502 NA 8.93E-06 mr1405_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
vg0920821502 NA 5.14E-10 mr1751_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
vg0920821502 NA 2.68E-06 mr1786_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