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Detailed information for vg0402757872:

Variant ID: vg0402757872 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2757872
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATCCAACGTTTGATCATTCGTCTTATTCAAAAAATTTATGTAATTATCATTTATTTTATTATAACTTGATTCGTCGTCAAATGTTCTTTAAGCATGAC[A/G]
TAAATATTTTCATATTTGCACAAAAATTTTGAATAAAACGAATGGTCAAACGTTGGTCGAAAAGTCAACGGCGTCATACATTAAAATACGGAGGGAGAAT

Reverse complement sequence

ATTCTCCCTCCGTATTTTAATGTATGACGCCGTTGACTTTTCGACCAACGTTTGACCATTCGTTTTATTCAAAATTTTTGTGCAAATATGAAAATATTTA[T/C]
GTCATGCTTAAAGAACATTTGACGACGAATCAAGTTATAATAAAATAAATGATAATTACATAAATTTTTTGAATAAGACGAATGATCAAACGTTGGATAA

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 66.10% 13.20% 1.31% 19.34% NA
All Indica  2759 68.60% 0.50% 1.23% 29.58% NA
All Japonica  1512 56.30% 39.00% 1.65% 3.04% NA
Aus  269 85.90% 0.70% 0.74% 12.64% NA
Indica I  595 97.00% 0.00% 0.00% 3.03% NA
Indica II  465 71.40% 0.90% 1.08% 26.67% NA
Indica III  913 49.30% 0.10% 1.97% 48.63% NA
Indica Intermediate  786 68.10% 1.30% 1.40% 29.26% NA
Temperate Japonica  767 90.20% 9.50% 0.13% 0.13% NA
Tropical Japonica  504 20.40% 67.30% 4.17% 8.13% NA
Japonica Intermediate  241 23.70% 73.40% 1.24% 1.66% NA
VI/Aromatic  96 90.60% 8.30% 0.00% 1.04% NA
Intermediate  90 66.70% 13.30% 1.11% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0402757872 A -> DEL N N silent_mutation Average:63.214; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N
vg0402757872 A -> G LOC_Os04g05470.1 intron_variant ; MODIFIER silent_mutation Average:63.214; most accessible tissue: Zhenshan97 root, score: 91.119 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402757872 NA 8.79E-07 mr1554 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
vg0402757872 NA 2.65E-09 mr1563 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
vg0402757872 NA 7.17E-07 mr1602 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
vg0402757872 NA 1.31E-09 mr1668 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
vg0402757872 NA 5.11E-07 mr1668 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
vg0402757872 NA 1.66E-09 mr1554_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
vg0402757872 NA 3.51E-06 mr1554_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
vg0402757872 6.28E-08 NA mr1563_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
vg0402757872 NA 1.80E-11 mr1563_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
vg0402757872 NA 8.44E-08 mr1668_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