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Detailed information for vg0429377757:

Variant ID: vg0429377757 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29377757
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATATATAGAAAAACTATTCTACACCCAAGCGGGTATAGAATAGCTATTCTATACCCCCTCTCTCCCAAGGGTCAAACCCACCTCCCACCTTAGTCAAA[G/T,A]
GTCAGTCAAAGCATCCCCACGTTGGTTAAAGCCCGGTCAAATCATCTACCAACTCCCCCCAAAAACCAATTCTTCTCATCTTTCGTCTTGCACGAACTCG

Reverse complement sequence

CGAGTTCGTGCAAGACGAAAGATGAGAAGAATTGGTTTTTGGGGGGAGTTGGTAGATGATTTGACCGGGCTTTAACCAACGTGGGGATGCTTTGACTGAC[C/A,T]
TTTGACTAAGGTGGGAGGTGGGTTTGACCCTTGGGAGAGAGGGGGTATAGAATAGCTATTCTATACCCGCTTGGGTGTAGAATAGTTTTTCTATATATAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.60% 12.90% 0.47% 0.00% A: 0.04%
All Indica  2759 95.90% 4.00% 0.04% 0.00% NA
All Japonica  1512 67.00% 31.70% 1.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 89.50% 10.40% 0.11% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 97.50% 1.30% 1.17% 0.00% NA
Tropical Japonica  504 22.80% 77.00% 0.20% 0.00% NA
Japonica Intermediate  241 62.20% 34.00% 3.73% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 77.80% 17.80% 2.22% 0.00% A: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0429377757 G -> A LOC_Os04g49230-LOC_Os04g49240 intergenic_region ; MODIFIER silent_mutation Average:47.828; most accessible tissue: Minghui63 root, score: 80.163 N N N N
vg0429377757 G -> T LOC_Os04g49230-LOC_Os04g49240 intergenic_region ; MODIFIER silent_mutation Average:47.828; most accessible tissue: Minghui63 root, score: 80.163 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429377757 NA 1.69E-07 mr1194 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
vg0429377757 NA 1.25E-07 mr1248 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
vg0429377757 NA 2.40E-06 mr1338 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
vg0429377757 NA 5.66E-14 mr1449 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
vg0429377757 NA 1.24E-08 mr1449 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
vg0429377757 NA 3.87E-07 mr1627 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
vg0429377757 NA 1.77E-06 mr1880 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
vg0429377757 1.80E-06 NA mr1124_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
vg0429377757 NA 3.68E-06 mr1194_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
vg0429377757 NA 3.29E-10 mr1769_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
vg0429377757 NA 4.19E-06 mr1786_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
vg0429377757 2.10E-06 NA mr1850_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