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Detailed information for vg0711410816:

Variant ID: vg0711410816 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 11410816
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGAAATAAATAGAGAATTTAAATATAGGATCAACATGCTCAAAGGAATTGTGTTTGGGATCTGTGTGACTTGCCTTGCAATAACGGGTCTTCAATTAA[C/T]
CTTCTTGAACACTTCCGAGGCACTTACGATCCTTCGAAACGACGGAAACGACAAGCTAACACGCAAAACGAGAAAAAAGACTAATAAAAACCAAATAAAC

Reverse complement sequence

GTTTATTTGGTTTTTATTAGTCTTTTTTCTCGTTTTGCGTGTTAGCTTGTCGTTTCCGTCGTTTCGAAGGATCGTAAGTGCCTCGGAAGTGTTCAAGAAG[G/A]
TTAATTGAAGACCCGTTATTGCAAGGCAAGTCACACAGATCCCAAACACAATTCCTTTGAGCATGTTGATCCTATATTTAAATTCTCTATTTATTTCAAC

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 40.80% 27.00% 13.50% 18.71% NA
All Indica  2759 50.00% 4.00% 15.80% 30.23% NA
All Japonica  1512 19.80% 74.40% 5.09% 0.66% NA
Aus  269 52.40% 3.00% 35.69% 8.92% NA
Indica I  595 40.50% 4.70% 7.56% 47.23% NA
Indica II  465 21.30% 6.70% 16.13% 55.91% NA
Indica III  913 69.40% 1.00% 19.72% 9.86% NA
Indica Intermediate  786 51.70% 5.20% 17.30% 25.83% NA
Temperate Japonica  767 33.10% 65.30% 0.52% 1.04% NA
Tropical Japonica  504 1.00% 85.90% 13.10% 0.00% NA
Japonica Intermediate  241 17.00% 79.30% 2.90% 0.83% NA
VI/Aromatic  96 84.40% 0.00% 14.58% 1.04% NA
Intermediate  90 28.90% 37.80% 16.67% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0711410816 C -> DEL N N silent_mutation Average:6.803; most accessible tissue: Callus, score: 11.104 N N N N
vg0711410816 C -> T LOC_Os07g19274.1 downstream_gene_variant ; 913.0bp to feature; MODIFIER silent_mutation Average:6.803; most accessible tissue: Callus, score: 11.104 N N N N
vg0711410816 C -> T LOC_Os07g19274-LOC_Os07g19290 intergenic_region ; MODIFIER silent_mutation Average:6.803; most accessible tissue: Callus, score: 11.104 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0711410816 NA 7.86E-08 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
vg0711410816 NA 3.58E-06 mr1192 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
vg0711410816 NA 1.61E-08 mr1677 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
vg0711410816 NA 3.66E-06 mr1167_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
vg0711410816 NA 1.15E-06 mr1269_2 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
vg0711410816 NA 2.07E-06 mr1289_2 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
vg0711410816 NA 1.89E-06 mr1405_2 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
vg0711410816 NA 1.47E-06 mr1418_2 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
vg0711410816 NA 6.49E-10 mr1479_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
vg0711410816 NA 2.23E-06 mr1488_2 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
vg0711410816 NA 1.41E-07 mr1662_2 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
vg0711410816 NA 7.45E-16 mr1726_2 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
vg0711410816 NA 3.66E-06 mr1726_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
vg0711410816 NA 6.93E-06 mr1741_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
vg0711410816 NA 9.65E-09 mr1765_2 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