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Detailed information for vg0604755502:

Variant ID: vg0604755502 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4755502
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAAATATGTGTAAATATGTTAAAAAAATGAGTTTGAGGTGAGTTTGGCTTTTTTTTAAATATGTTAAAAAAATTAAAGGGTGGTGGGTCTTTTAGGTT[G/A]
GAGTGGAGCTATGGAGCAGAAAAAAAAACCCAGCTCCACCCTTTGTTCTCTTTGACTGCCCGATATACAGCTTGAATTTCTAGAGCATTCATAACACAAA

Reverse complement sequence

TTTGTGTTATGAATGCTCTAGAAATTCAAGCTGTATATCGGGCAGTCAAAGAGAACAAAGGGTGGAGCTGGGTTTTTTTTTCTGCTCCATAGCTCCACTC[C/T]
AACCTAAAAGACCCACCACCCTTTAATTTTTTTAACATATTTAAAAAAAAGCCAAACTCACCTCAAACTCATTTTTTTAACATATTTACACATATTTTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 5.20% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 84.50% 15.50% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 75.90% 24.10% 0.00% 0.00% NA
Tropical Japonica  504 96.60% 3.40% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg0604755502 G -> A LOC_Os06g09410.1 upstream_gene_variant ; 1058.0bp to feature; MODIFIER silent_mutation Average:48.471; most accessible tissue: Callus, score: 70.318 N N N N
vg0604755502 G -> A LOC_Os06g09400-LOC_Os06g09410 intergenic_region ; MODIFIER silent_mutation Average:48.471; most accessible tissue: Callus, score: 70.318 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604755502 NA 4.37E-07 mr1062 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
vg0604755502 NA 2.80E-08 mr1585 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
vg0604755502 9.18E-07 9.18E-07 mr1608 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
vg0604755502 NA 9.73E-06 mr1049_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
vg0604755502 NA 8.50E-06 mr1305_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
vg0604755502 NA 2.01E-07 mr1585_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