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Detailed information for vg0613624979:

Variant ID: vg0613624979 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13624979
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGGTTTGAAATGTAGCTTAAATGGAAGAATTGATAGATTGGCCGCAGATTTAATGTAGTTCCTAGGTTATCAAACCATCACAGAATACAAAATGCATGG[G/A]
GAATTATGGTGGATTGGTCAGTGTAGTCCATGGACGCAACCGACCTAGACACCAAAATTCTCCATGCATTTTATATTCTGTCATTCTTTGATAATTAAGG

Reverse complement sequence

CCTTAATTATCAAAGAATGACAGAATATAAAATGCATGGAGAATTTTGGTGTCTAGGTCGGTTGCGTCCATGGACTACACTGACCAATCCACCATAATTC[C/T]
CCATGCATTTTGTATTCTGTGATGGTTTGATAACCTAGGAACTACATTAAATCTGCGGCCAATCTATCAATTCTTCCATTTAAGCTACATTTCAAACCCT

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 64.50% 35.30% 0.28% 0.00% NA
All Indica  2759 95.10% 4.50% 0.40% 0.00% NA
All Japonica  1512 7.30% 92.60% 0.07% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 93.30% 6.40% 0.34% 0.00% NA
Indica II  465 96.10% 3.00% 0.86% 0.00% NA
Indica III  913 97.30% 2.30% 0.44% 0.00% NA
Indica Intermediate  786 93.30% 6.60% 0.13% 0.00% NA
Temperate Japonica  767 3.50% 96.30% 0.13% 0.00% NA
Tropical Japonica  504 13.30% 86.70% 0.00% 0.00% NA
Japonica Intermediate  241 7.10% 92.90% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 50.00% 48.90% 1.11% 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
vg0613624979 G -> A LOC_Os06g23330.1 upstream_gene_variant ; 1549.0bp to feature; MODIFIER silent_mutation Average:30.351; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0613624979 G -> A LOC_Os06g23340.1 upstream_gene_variant ; 324.0bp to feature; MODIFIER silent_mutation Average:30.351; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0613624979 G -> A LOC_Os06g23320.1 downstream_gene_variant ; 2560.0bp to feature; MODIFIER silent_mutation Average:30.351; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N
vg0613624979 G -> A LOC_Os06g23330-LOC_Os06g23340 intergenic_region ; MODIFIER silent_mutation Average:30.351; most accessible tissue: Minghui63 young leaf, score: 45.896 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613624979 NA 2.80E-06 mr1020 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
vg0613624979 3.22E-07 3.22E-07 mr1032 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
vg0613624979 3.13E-12 6.47E-83 mr1033 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
vg0613624979 1.79E-06 6.29E-11 mr1033 Ind_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
vg0613624979 4.52E-06 4.15E-12 mr1033 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
vg0613624979 NA 2.40E-06 mr1082 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
vg0613624979 6.33E-06 6.33E-06 mr1165 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
vg0613624979 4.79E-08 3.20E-44 mr1176 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
vg0613624979 NA 4.20E-06 mr1176 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
vg0613624979 7.99E-06 5.97E-08 mr1176 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
vg0613624979 1.17E-07 1.17E-07 mr1478 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
vg0613624979 4.79E-07 4.79E-07 mr1536 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
vg0613624979 NA 1.28E-07 mr1971 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
vg0613624979 3.05E-09 3.71E-103 mr1033_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
vg0613624979 NA 1.54E-14 mr1033_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
vg0613624979 3.01E-07 6.20E-16 mr1033_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
vg0613624979 6.67E-06 4.94E-09 mr1536_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
vg0613624979 NA 1.86E-07 mr1548_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