Search for Variation information by Variation ID:

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

Detailed information for vg0710366378:

Variant ID: vg0710366378 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10366378
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, C: 0.07, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGAACAGATATTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAACGAAGAAGAGGGGAATGAGGATCCAAACCAGTACTTGAACGAGGAAG[G/C]
GAACGTGAAGAAGGATGCGGAGGGGAACCAGGAGGGGAACGTGGAGAGGGATGTGGAGGGGAACCAGGAGGAGGAGGCTAGTGGAAGTCAACCCTCCGCT

Reverse complement sequence

AGCGGAGGGTTGACTTCCACTAGCCTCCTCCTCCTGGTTCCCCTCCACATCCCTCTCCACGTTCCCCTCCTGGTTCCCCTCCGCATCCTTCTTCACGTTC[C/G]
CTTCCTCGTTCAAGTACTGGTTTGGATCCTCATTCCCCTCTTCTTCGTTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAATATCTGTTCCTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.30% 40.60% 10.66% 7.51% NA
All Indica  2759 67.50% 8.20% 13.19% 11.13% NA
All Japonica  1512 0.90% 95.60% 0.93% 2.65% NA
Aus  269 13.80% 62.80% 22.30% 1.12% NA
Indica I  595 68.10% 6.90% 16.13% 8.91% NA
Indica II  465 61.50% 5.20% 16.13% 17.20% NA
Indica III  913 75.00% 4.70% 9.53% 10.73% NA
Indica Intermediate  786 62.00% 14.90% 13.49% 9.67% NA
Temperate Japonica  767 1.00% 98.00% 0.65% 0.26% NA
Tropical Japonica  504 0.40% 91.10% 1.19% 7.34% NA
Japonica Intermediate  241 1.20% 97.10% 1.24% 0.41% NA
VI/Aromatic  96 9.40% 34.40% 56.25% 0.00% NA
Intermediate  90 31.10% 50.00% 13.33% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0710366378 G -> DEL LOC_Os07g17530.1 N frameshift_variant Average:23.806; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N
vg0710366378 G -> C LOC_Os07g17530.1 missense_variant ; p.Gly914Ala; MODERATE nonsynonymous_codon ; G914A Average:23.806; most accessible tissue: Minghui63 young leaf, score: 32.638 benign 1.408 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710366378 NA 2.87E-21 mr1051 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
vg0710366378 2.72E-06 4.99E-37 mr1828 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