Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1005451907:

Variant ID: vg1005451907 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5451907
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAATGACAGATTATTTGGGCTTAATAAATTCACCTCGCAGTTTCTAGGCGGAATCTGTAATTTGTTTTGTTATTAGTCCATGTTTAATATTTCAAATAT[A/G]
TATGTGTATATCCGATGTGACACGCCAAAATTTTCATGCATGACCTAAACATGCCCTAACTTGTGAAATGAAGTTATTTCTTCAAAATATTTAGTTGCAA

Reverse complement sequence

TTGCAACTAAATATTTTGAAGAAATAACTTCATTTCACAAGTTAGGGCATGTTTAGGTCATGCATGAAAATTTTGGCGTGTCACATCGGATATACACATA[T/C]
ATATTTGAAATATTAAACATGGACTAATAACAAAACAAATTACAGATTCCGCCTAGAAACTGCGAGGTGAATTTATTAAGCCCAAATAATCTGTCATTAG

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 78.60% 21.40% 0.02% 0.00% NA
All Indica  2759 98.80% 1.20% 0.04% 0.00% NA
All Japonica  1512 38.60% 61.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.40% 0.13% 0.00% NA
Temperate Japonica  767 26.60% 73.40% 0.00% 0.00% NA
Tropical Japonica  504 50.60% 49.40% 0.00% 0.00% NA
Japonica Intermediate  241 51.90% 48.10% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 68.90% 31.10% 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
vg1005451907 A -> G LOC_Os10g10030.1 upstream_gene_variant ; 2833.0bp to feature; MODIFIER silent_mutation Average:28.407; most accessible tissue: Minghui63 root, score: 52.955 N N N N
vg1005451907 A -> G LOC_Os10g10030-LOC_Os10g10040 intergenic_region ; MODIFIER silent_mutation Average:28.407; most accessible tissue: Minghui63 root, score: 52.955 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005451907 8.72E-15 4.98E-28 mr1768 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
vg1005451907 4.83E-07 1.20E-10 mr1768 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
vg1005451907 8.99E-22 6.39E-47 mr1768_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
vg1005451907 1.04E-08 7.34E-12 mr1768_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