Search for Variation information by Variation ID:

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

Detailed information for vg0718167360:

Variant ID: vg0718167360 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 18167360
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTTTGAAATATATACATTTCTCCCTACTGCCTAACACACTAGTAAAAAATTTATGCACGTCTTATGTACAACAAAATATAATACTAAACTTTTTCTA[T/C]
ATTCAAACTACATTCATACTATATATACTTCTAACTTAAGTGGTACCTAAAATTTCTAAACTTACCATATAACCGAACTATTTACATGTAATATATGCAC

Reverse complement sequence

GTGCATATATTACATGTAAATAGTTCGGTTATATGGTAAGTTTAGAAATTTTAGGTACCACTTAAGTTAGAAGTATATATAGTATGAATGTAGTTTGAAT[A/G]
TAGAAAAAGTTTAGTATTATATTTTGTTGTACATAAGACGTGCATAAATTTTTTACTAGTGTGTTAGGCAGTAGGGAGAAATGTATATATTTCAAAATTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.80% 1.90% 0.25% 0.00% NA
All Indica  2759 99.80% 0.10% 0.04% 0.00% NA
All Japonica  1512 93.50% 5.80% 0.73% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 89.80% 8.90% 1.30% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 92.50% 7.50% 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
vg0718167360 T -> C LOC_Os07g30700.1 upstream_gene_variant ; 908.0bp to feature; MODIFIER silent_mutation Average:52.822; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0718167360 T -> C LOC_Os07g30690.1 downstream_gene_variant ; 4966.0bp to feature; MODIFIER silent_mutation Average:52.822; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0718167360 T -> C LOC_Os07g30690-LOC_Os07g30700 intergenic_region ; MODIFIER silent_mutation Average:52.822; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0718167360 1.93E-06 NA mr1980 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