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Detailed information for vg0401189541:

Variant ID: vg0401189541 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1189541
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGTCCTCCTGGAAACTGCAAGTCAGTTCAGTGAGATACAGAAGTACACAGACGAGGAGTAAGTGTAGTAGCTAGGAAATCAATACTAATTACCATATG[A/G]
TTCAATACATATACATTTTTTTCAATTAAGATAATAGAAAAATTCTGGCCTTTACCTAGAAGTAAGCTCAAGTCAAATTGTTATTTCGTACCCCTCCGTT

Reverse complement sequence

AACGGAGGGGTACGAAATAACAATTTGACTTGAGCTTACTTCTAGGTAAAGGCCAGAATTTTTCTATTATCTTAATTGAAAAAAATGTATATGTATTGAA[T/C]
CATATGGTAATTAGTATTGATTTCCTAGCTACTACACTTACTCCTCGTCTGTGTACTTCTGTATCTCACTGAACTGACTTGCAGTTTCCAGGAGGACAAA

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 86.80% 13.10% 0.08% 0.00% NA
All Indica  2759 77.60% 22.30% 0.14% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 36.50% 63.20% 0.34% 0.00% NA
Indica II  465 92.50% 7.50% 0.00% 0.00% NA
Indica III  913 89.20% 10.70% 0.11% 0.00% NA
Indica Intermediate  786 86.40% 13.50% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0401189541 A -> G LOC_Os04g02960.1 intron_variant ; MODIFIER silent_mutation Average:45.09; most accessible tissue: Callus, score: 91.697 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401189541 NA 5.80E-11 mr1565 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
vg0401189541 NA 2.97E-06 mr1842 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
vg0401189541 NA 3.17E-06 mr1201_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
vg0401189541 NA 2.66E-06 mr1201_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
vg0401189541 1.19E-07 NA mr1565_2 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
vg0401189541 4.60E-09 2.95E-16 mr1565_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
vg0401189541 NA 1.66E-08 mr1707_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