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Detailed information for vg1000062161:

Variant ID: vg1000062161 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 62161
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GACAAATTTATTAAGCCTAATTAATCTGTCATTAGCAAATATTTACTGTAGCACCATATTATTAAATCATGGCACAATTAGGATTAAAAGATTTGTCTCA[C/T]
AATTTACACGCAATCTGTGTAATTGGTTTTTTTCCTACATTTAATACTCCACACATGTGTCCAAACATTCGATGTTAAAGCATAAAAATTTTTGTTTGGG

Reverse complement sequence

CCCAAACAAAAATTTTTATGCTTTAACATCGAATGTTTGGACACATGTGTGGAGTATTAAATGTAGGAAAAAAACCAATTACACAGATTGCGTGTAAATT[G/A]
TGAGACAAATCTTTTAATCCTAATTGTGCCATGATTTAATAATATGGTGCTACAGTAAATATTTGCTAATGACAGATTAATTAGGCTTAATAAATTTGTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.40% 0.28% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.40% 3.90% 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  465 100.00% 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 91.40% 7.20% 1.43% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 8.30% 1.04% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg1000062161 C -> T LOC_Os10g01044.1 upstream_gene_variant ; 3824.0bp to feature; MODIFIER silent_mutation Average:32.514; most accessible tissue: Zhenshan97 young leaf, score: 39.843 N N N N
vg1000062161 C -> T LOC_Os10g01060.1 upstream_gene_variant ; 4958.0bp to feature; MODIFIER silent_mutation Average:32.514; most accessible tissue: Zhenshan97 young leaf, score: 39.843 N N N N
vg1000062161 C -> T LOC_Os10g01044.2 upstream_gene_variant ; 3824.0bp to feature; MODIFIER silent_mutation Average:32.514; most accessible tissue: Zhenshan97 young leaf, score: 39.843 N N N N
vg1000062161 C -> T LOC_Os10g01044.3 upstream_gene_variant ; 3823.0bp to feature; MODIFIER silent_mutation Average:32.514; most accessible tissue: Zhenshan97 young leaf, score: 39.843 N N N N
vg1000062161 C -> T LOC_Os10g01044-LOC_Os10g01060 intergenic_region ; MODIFIER silent_mutation Average:32.514; most accessible tissue: Zhenshan97 young leaf, score: 39.843 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000062161 1.01E-07 1.88E-12 Awn_length Jap_All YES 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
vg1000062161 1.36E-06 1.36E-06 mr1470 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