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Detailed information for vg0410565141:

Variant ID: vg0410565141 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10565141
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAAATTCCATCTTCTATTTCTTTCAAAGTGCACAGAAATTGCAAAGTAAGCAAAAGAGAACCAGGCTCATCTACCACAACAAATCTCTGCCAACCAACA[A/G]
CTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAGCATACTCCCGGTCACTCAGCATGTA

Reverse complement sequence

TACATGCTGAGTGACCGGGAGTATGCTCACACACGAGAATACTCTCCGGAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAG[T/C]
TGTTGGTTGGCAGAGATTTGTTGTGGTAGATGAGCCTGGTTCTCTTTTGCTTACTTTGCAATTTCTGTGCACTTTGAAAGAAATAGAAGATGGAATTTCC

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 21.40% 17.80% 0.28% 60.54% NA
All Indica  2759 2.60% 5.10% 0.40% 91.84% NA
All Japonica  1512 60.80% 38.40% 0.00% 0.86% NA
Aus  269 0.70% 0.00% 0.37% 98.88% NA
Indica I  595 4.90% 0.20% 0.34% 94.62% NA
Indica II  465 2.40% 22.60% 0.65% 74.41% NA
Indica III  913 0.70% 0.90% 0.11% 98.36% NA
Indica Intermediate  786 3.40% 3.40% 0.64% 92.49% NA
Temperate Japonica  767 95.80% 3.80% 0.00% 0.39% NA
Tropical Japonica  504 4.00% 94.80% 0.00% 1.19% NA
Japonica Intermediate  241 68.00% 30.30% 0.00% 1.66% NA
VI/Aromatic  96 0.00% 86.50% 0.00% 13.54% NA
Intermediate  90 21.10% 38.90% 1.11% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0410565141 A -> DEL LOC_Os04g19010.1 N frameshift_variant Average:7.615; most accessible tissue: Callus, score: 15.368 N N N N
vg0410565141 A -> G LOC_Os04g19010.1 missense_variant ; p.Val61Ala; MODERATE nonsynonymous_codon ; V61A Average:7.615; most accessible tissue: Callus, score: 15.368 benign -0.121 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410565141 NA 3.82E-06 mr1045 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
vg0410565141 NA 2.17E-06 mr1090 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
vg0410565141 NA 3.42E-06 mr1121 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
vg0410565141 NA 9.29E-08 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
vg0410565141 NA 4.91E-07 mr1206 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
vg0410565141 NA 5.73E-07 mr1403 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
vg0410565141 NA 3.88E-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
vg0410565141 NA 3.88E-11 mr1454 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
vg0410565141 NA 3.67E-07 mr1715 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
vg0410565141 NA 3.57E-07 mr1739 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
vg0410565141 NA 3.46E-13 mr1789 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
vg0410565141 NA 6.15E-06 mr1844 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
vg0410565141 NA 2.12E-09 mr1880 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
vg0410565141 NA 9.37E-12 mr1593_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