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Detailed information for vg0619155351:

Variant ID: vg0619155351 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19155351
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.03, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GTCAACACTGACAGTGCAGCCCATCTACCTTCTCATGCCCTCAAGGAGACCAAAGAAGCCCTAGGTCTCCTTGACACAAAAGATAAGGAAGTTCCTATGG[G/A]
CGGGGACAAGGGCCATCACAGGGGGGAAATGCATGATTAACTGGAAAAAGACGTGCATCCCAACCACACCAGGAGGACTGGGAGTTCTCAATATGCAGAA

Reverse complement sequence

TTCTGCATATTGAGAACTCCCAGTCCTCCTGGTGTGGTTGGGATGCACGTCTTTTTCCAGTTAATCATGCATTTCCCCCCTGTGATGGCCCTTGTCCCCG[C/T]
CCATAGGAACTTCCTTATCTTTTGTGTCAAGGAGACCTAGGGCTTCTTTGGTCTCCTTGAGGGCATGAGAAGGTAGATGGGCTGCACTGTCAGTGTTGAC

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 50.00% 48.30% 0.36% 1.33% NA
All Indica  2759 79.20% 20.30% 0.33% 0.18% NA
All Japonica  1512 2.90% 93.30% 0.33% 3.44% NA
Aus  269 34.90% 65.10% 0.00% 0.00% NA
Indica I  595 79.80% 19.00% 0.84% 0.34% NA
Indica II  465 93.30% 6.50% 0.00% 0.22% NA
Indica III  913 79.30% 20.40% 0.22% 0.11% NA
Indica Intermediate  786 70.40% 29.30% 0.25% 0.13% NA
Temperate Japonica  767 4.20% 91.70% 0.52% 3.65% NA
Tropical Japonica  504 0.80% 97.80% 0.00% 1.39% NA
Japonica Intermediate  241 3.30% 89.20% 0.41% 7.05% NA
VI/Aromatic  96 2.10% 92.70% 1.04% 4.17% NA
Intermediate  90 42.20% 53.30% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619155351 G -> A LOC_Os06g32900.1 missense_variant ; p.Gly924Asp; MODERATE nonsynonymous_codon ; G924D Average:56.661; most accessible tissue: Zhenshan97 young leaf, score: 82.763 unknown unknown DELETERIOUS 0.00
vg0619155351 G -> DEL LOC_Os06g32900.1 N frameshift_variant Average:56.661; most accessible tissue: Zhenshan97 young leaf, score: 82.763 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619155351 NA 5.88E-08 mr1354 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
vg0619155351 NA 6.08E-06 mr1269_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
vg0619155351 NA 8.97E-06 mr1291_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
vg0619155351 NA 6.22E-06 mr1291_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
vg0619155351 NA 5.81E-07 mr1346_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
vg0619155351 NA 7.41E-06 mr1428_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
vg0619155351 4.77E-06 4.77E-06 mr1477_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
vg0619155351 NA 7.75E-06 mr1479_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