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Detailed information for vg0909067656:

Variant ID: vg0909067656 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9067656
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCTTTTGATGATTACTGCAGGAAGGAAGGCATCGTTAGGCATCACACCATCCCGTACACTCCACAGCAGAATGGTGTGGCTGAGCGCATGAATAGAACC[A/G]
TCATCTCCAAGGCTCGTTGTATGCTGTCCAACGCTCGCATGAGCAAGCGTTTTTGGGCAGAGGCTACTAACACCGCCTGCTACTTAATCAACAGGTCGCC

Reverse complement sequence

GGCGACCTGTTGATTAAGTAGCAGGCGGTGTTAGTAGCCTCTGCCCAAAAACGCTTGCTCATGCGAGCGTTGGACAGCATACAACGAGCCTTGGAGATGA[T/C]
GGTTCTATTCATGCGCTCAGCCACACCATTCTGCTGTGGAGTGTACGGGATGGTGTGATGCCTAACGATGCCTTCCTTCCTGCAGTAATCATCAAAAGCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.50% 3.50% 0.00% 0.00% NA
All Indica  2759 98.20% 1.80% 0.00% 0.00% NA
All Japonica  1512 92.30% 7.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.00% 4.00% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 94.10% 5.90% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 25.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0909067656 A -> G LOC_Os09g15030.1 missense_variant ; p.Ile368Val; MODERATE nonsynonymous_codon ; I368V Average:19.944; most accessible tissue: Zhenshan97 panicle, score: 39.652 unknown unknown TOLERATED 0.17

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909067656 NA 6.49E-08 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
vg0909067656 3.58E-06 3.58E-06 mr1297 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
vg0909067656 NA 5.91E-06 mr1510 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
vg0909067656 NA 7.25E-06 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
vg0909067656 NA 4.45E-06 mr1702_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