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Detailed information for vg0905696575:

Variant ID: vg0905696575 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5696575
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTGAGAGGATGTGGAGGGGATGTCCCGAGGCACAGACCCGCGCTTGGGCAAGCGCAAGGAAAGAGCGGTATGTGGCTCCTCGCACACAAACCGAAGGT[G/A]
AGTGACATGTTCAATCATCCGCATTATATGAGGAGCATAGGGAAGCCCTCGCTTATACTGAAGAGAAGCCATGCGGATTTCCTGCCAAACAAATAAAAAG

Reverse complement sequence

CTTTTTATTTGTTTGGCAGGAAATCCGCATGGCTTCTCTTCAGTATAAGCGAGGGCTTCCCTATGCTCCTCATATAATGCGGATGATTGAACATGTCACT[C/T]
ACCTTCGGTTTGTGTGCGAGGAGCCACATACCGCTCTTTCCTTGCGCTTGCCCAAGCGCGGGTCTGTGCCTCGGGACATCCCCTCCACATCCTCTCAGCC

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 86.60% 5.10% 2.05% 6.31% NA
All Indica  2759 98.50% 0.10% 1.34% 0.11% NA
All Japonica  1512 66.40% 15.30% 2.91% 15.41% NA
Aus  269 98.90% 0.00% 1.12% 0.00% NA
Indica I  595 97.60% 0.20% 2.02% 0.17% NA
Indica II  465 98.30% 0.20% 1.51% 0.00% NA
Indica III  913 99.10% 0.00% 0.77% 0.11% NA
Indica Intermediate  786 98.50% 0.00% 1.40% 0.13% NA
Temperate Japonica  767 92.20% 0.30% 1.17% 6.39% NA
Tropical Japonica  504 35.30% 43.70% 5.95% 15.08% NA
Japonica Intermediate  241 49.40% 3.70% 2.07% 44.81% NA
VI/Aromatic  96 32.30% 0.00% 4.17% 63.54% NA
Intermediate  90 81.10% 7.80% 10.00% 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
vg0905696575 G -> DEL LOC_Os09g10420.1 N frameshift_variant Average:57.298; most accessible tissue: Minghui63 young leaf, score: 71.254 N N N N
vg0905696575 G -> A LOC_Os09g10420.1 missense_variant ; p.His241Tyr; MODERATE nonsynonymous_codon ; H241Y Average:57.298; most accessible tissue: Minghui63 young leaf, score: 71.254 unknown unknown DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905696575 NA 5.26E-07 mr1082 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
vg0905696575 NA 8.35E-07 mr1083 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
vg0905696575 NA 6.57E-06 mr1925 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
vg0905696575 1.04E-06 1.04E-06 mr1076_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
vg0905696575 4.94E-06 1.25E-08 mr1082_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
vg0905696575 2.98E-06 8.75E-09 mr1083_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
vg0905696575 NA 6.94E-07 mr1226_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
vg0905696575 1.06E-06 1.02E-07 mr1408_2 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
vg0905696575 NA 7.40E-08 mr1551_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
vg0905696575 NA 6.24E-09 mr1916_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