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Detailed information for vg0909179226:

Variant ID: vg0909179226 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9179226
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGACCAAACGGGAGATTAACGCTGTTCAGCCCAATACGCACCAATATCTTCGGTGGTCGGAGACAACAATCAAGTTTGACCGCTCGGATCATCCAGACC[A/G]
AGTGGTCCACCCGGGGCGGTACCCCCTGGTACTAGACCCAGTGGTTCGCAACGTCAAGCTTCGCAGATCCCTCATCGATGGCGGCAGTGCACTCAACATC

Reverse complement sequence

GATGTTGAGTGCACTGCCGCCATCGATGAGGGATCTGCGAAGCTTGACGTTGCGAACCACTGGGTCTAGTACCAGGGGGTACCGCCCCGGGTGGACCACT[T/C]
GGTCTGGATGATCCGAGCGGTCAAACTTGATTGTTGTCTCCGACCACCGAAGATATTGGTGCGTATTGGGCTGAACAGCGTTAATCTCCCGTTTGGTCAG

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 45.50% 0.10% 2.56% 51.84% NA
All Indica  2759 23.10% 0.10% 2.46% 74.37% NA
All Japonica  1512 80.10% 0.00% 2.18% 17.72% NA
Aus  269 71.70% 0.40% 1.86% 26.02% NA
Indica I  595 22.70% 0.20% 1.85% 75.29% NA
Indica II  465 17.20% 0.00% 1.94% 80.86% NA
Indica III  913 26.20% 0.10% 3.18% 70.54% NA
Indica Intermediate  786 23.20% 0.10% 2.42% 74.30% NA
Temperate Japonica  767 77.60% 0.00% 2.48% 19.95% NA
Tropical Japonica  504 88.10% 0.00% 1.98% 9.92% NA
Japonica Intermediate  241 71.40% 0.00% 1.66% 26.97% NA
VI/Aromatic  96 49.00% 0.00% 12.50% 38.54% NA
Intermediate  90 71.10% 0.00% 3.33% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0909179226 A -> G LOC_Os09g15120.1 missense_variant ; p.Gln690Arg; MODERATE nonsynonymous_codon ; Q690R Average:11.91; most accessible tissue: Callus, score: 44.688 unknown unknown TOLERATED 1.00
vg0909179226 A -> DEL LOC_Os09g15120.1 N frameshift_variant Average:11.91; most accessible tissue: Callus, score: 44.688 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909179226 NA 7.41E-06 mr1321_2 Ind_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
vg0909179226 NA 1.22E-09 mr1338_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
vg0909179226 NA 5.26E-07 mr1439_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
vg0909179226 1.40E-06 6.44E-08 mr1439_2 Ind_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
vg0909179226 NA 2.86E-06 mr1576_2 Ind_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
vg0909179226 NA 9.46E-06 mr1836_2 Ind_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