Search for Variation information by Variation ID:

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

Detailed information for vg0705477376:

Variant ID: vg0705477376 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 5477376
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTAATATTTTTTAATAATCGAGCTAAAAGTAAAAATTATATTAGTTATTAACAACAAATAAAACTGGTTTGTCAAGAGAAATAAAATTAGTAGACTCT[G/A]
TATGAGATTGTGGATGAAATATGATCTACCGCACTTTGATTATATGGATGAATATATGTTAATTATTATAAAAATGATGGATATATATATGTTAAAAATA

Reverse complement sequence

TATTTTTAACATATATATATCCATCATTTTTATAATAATTAACATATATTCATCCATATAATCAAAGTGCGGTAGATCATATTTCATCCACAATCTCATA[C/T]
AGAGTCTACTAATTTTATTTCTCTTGACAAACCAGTTTTATTTGTTGTTAATAACTAATATAATTTTTACTTTTAGCTCGATTATTAAAAAATATTAAAA

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 98.90% 1.00% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.60% 3.20% 0.13% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.40% 5.30% 0.26% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0705477376 G -> A LOC_Os07g10190.1 upstream_gene_variant ; 3064.0bp to feature; MODIFIER silent_mutation Average:19.609; most accessible tissue: Zhenshan97 root, score: 25.639 N N N N
vg0705477376 G -> A LOC_Os07g10170.1 downstream_gene_variant ; 2443.0bp to feature; MODIFIER silent_mutation Average:19.609; most accessible tissue: Zhenshan97 root, score: 25.639 N N N N
vg0705477376 G -> A LOC_Os07g10180.1 downstream_gene_variant ; 802.0bp to feature; MODIFIER silent_mutation Average:19.609; most accessible tissue: Zhenshan97 root, score: 25.639 N N N N
vg0705477376 G -> A LOC_Os07g10170-LOC_Os07g10180 intergenic_region ; MODIFIER silent_mutation Average:19.609; most accessible tissue: Zhenshan97 root, score: 25.639 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0705477376 8.16E-07 1.56E-10 mr1757 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
vg0705477376 2.02E-15 1.58E-17 mr1549_2 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
vg0705477376 8.96E-07 1.50E-07 mr1550_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
vg0705477376 3.82E-11 1.24E-13 mr1757_2 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