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Detailed information for vg0429371515:

Variant ID: vg0429371515 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29371515
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAATTTTAATAATTATTTTTACCGGGTTGTAGTGTTTTAGTTGCAATTAGTTTTTTAACTAAAAATTGAAAAACAATTTATTGATTGATTAAAATATATC[A/C]
TTTGTACTTGTCTTTTCCAGTATATTCACAGTAGATATTAAAAATACAAACACTACAATCTAGTAATGTTATTTTGACTTATTCTAATGTTATAATGGGG

Reverse complement sequence

CCCCATTATAACATTAGAATAAGTCAAAATAACATTACTAGATTGTAGTGTTTGTATTTTTAATATCTACTGTGAATATACTGGAAAAGACAAGTACAAA[T/G]
GATATATTTTAATCAATCAATAAATTGTTTTTCAATTTTTAGTTAAAAAACTAATTGCAACTAAAACACTACAACCCGGTAAAAATAATTATTAAAATTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.00% 16.30% 0.51% 0.13% NA
All Indica  2759 97.80% 1.50% 0.47% 0.22% NA
All Japonica  1512 52.50% 47.00% 0.53% 0.00% NA
Aus  269 98.10% 1.50% 0.37% 0.00% NA
Indica I  595 97.80% 2.00% 0.17% 0.00% NA
Indica II  465 97.40% 0.40% 1.08% 1.08% NA
Indica III  913 99.20% 0.40% 0.33% 0.00% NA
Indica Intermediate  786 96.30% 3.10% 0.51% 0.13% NA
Temperate Japonica  767 16.30% 82.90% 0.78% 0.00% NA
Tropical Japonica  504 94.20% 5.80% 0.00% 0.00% NA
Japonica Intermediate  241 80.50% 18.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 17.80% 2.22% 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
vg0429371515 A -> C LOC_Os04g49230.1 upstream_gene_variant ; 3000.0bp to feature; MODIFIER silent_mutation Average:13.651; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0429371515 A -> C LOC_Os04g49230-LOC_Os04g49240 intergenic_region ; MODIFIER silent_mutation Average:13.651; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0429371515 A -> DEL N N silent_mutation Average:13.651; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429371515 3.25E-06 NA Awn_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0429371515 NA 8.84E-06 mr1180 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
vg0429371515 NA 9.63E-13 mr1182 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
vg0429371515 NA 5.73E-06 mr1182 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
vg0429371515 NA 8.39E-07 mr1183 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
vg0429371515 NA 5.46E-11 mr1282 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
vg0429371515 NA 1.84E-08 mr1330 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
vg0429371515 NA 7.08E-07 mr1503 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
vg0429371515 NA 4.71E-07 mr1617 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
vg0429371515 NA 3.98E-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
vg0429371515 NA 1.12E-09 mr1658 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
vg0429371515 NA 9.87E-06 mr1826 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
vg0429371515 NA 1.59E-08 mr1057_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
vg0429371515 NA 5.17E-13 mr1182_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
vg0429371515 NA 1.69E-07 mr1182_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
vg0429371515 NA 1.08E-10 mr1282_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
vg0429371515 NA 2.52E-06 mr1282_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
vg0429371515 NA 2.62E-06 mr1730_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