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Detailed information for vg0711409773:

Variant ID: vg0711409773 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 11409773
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


TGGATAAGCCGAGTCGAGTAATAAAACATTGTTGAAATTGTCGTTTTGCCAGTTGAGGTAAATCTTGGCTCTCTTCGGTATTTCAAGCAAGACGACTTGT[T/C]
AGTTGAAGATTACAAGACCTTGATGGGAAGCAATTTTGAAGACGTCATCGACAAGCGTTTGCAGACTTTGAAGGAGATGAAGGCACTTCAAGATGGTGTT

Reverse complement sequence

AACACCATCTTGAAGTGCCTTCATCTCCTTCAAAGTCTGCAAACGCTTGTCGATGACGTCTTCAAAATTGCTTCCCATCAAGGTCTTGTAATCTTCAACT[A/G]
ACAAGTCGTCTTGCTTGAAATACCGAAGAGAGCCAAGATTTACCTCAACTGGCAAAACGACAATTTCAACAATGTTTTATTACTCGACTCGGCTTATCCA

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 27.80% 21.90% 2.37% 47.84% NA
All Indica  2759 5.00% 18.60% 2.46% 73.90% NA
All Japonica  1512 74.50% 24.00% 0.13% 1.32% NA
Aus  269 4.10% 21.90% 14.13% 59.85% NA
Indica I  595 5.20% 33.10% 1.34% 60.34% NA
Indica II  465 9.20% 10.80% 4.30% 75.70% NA
Indica III  913 2.20% 6.20% 3.40% 88.17% NA
Indica Intermediate  786 5.60% 26.70% 1.15% 66.54% NA
Temperate Japonica  767 65.60% 33.10% 0.26% 1.04% NA
Tropical Japonica  504 85.90% 13.30% 0.00% 0.79% NA
Japonica Intermediate  241 79.30% 17.40% 0.00% 3.32% NA
VI/Aromatic  96 3.10% 86.50% 0.00% 10.42% NA
Intermediate  90 41.10% 20.00% 4.44% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0711409773 T -> DEL LOC_Os07g19274.1 N frameshift_variant Average:7.325; most accessible tissue: Callus, score: 17.943 N N N N
vg0711409773 T -> C LOC_Os07g19274.1 missense_variant ; p.Leu524Ser; MODERATE nonsynonymous_codon ; L524S Average:7.325; most accessible tissue: Callus, score: 17.943 benign 0.082 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0711409773 NA 4.79E-09 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0711409773 NA 3.64E-06 mr1236 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
vg0711409773 1.90E-06 1.90E-06 mr1270 Ind_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
vg0711409773 3.00E-06 3.00E-06 mr1575 Ind_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
vg0711409773 NA 1.90E-07 mr1624_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