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Detailed information for vg0317440491:

Variant ID: vg0317440491 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17440491
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATAAAAGTAATTTATACTCTCTCCATCTACTTTTGATAAGCATATTTTTAAATCTGAAAAATTTATTTTTGATAGGCATATTTCAATTCAACAACTTAT[C/T]
ATCTTAATGACTTTCTTGGATTTAATGCGTGACTCTCCATTCTTCCACACAAGATTGGCTACATGGGCATCGAGAAATGTAAATATTAATAAATCACTTG

Reverse complement sequence

CAAGTGATTTATTAATATTTACATTTCTCGATGCCCATGTAGCCAATCTTGTGTGGAAGAATGGAGAGTCACGCATTAAATCCAAGAAAGTCATTAAGAT[G/A]
ATAAGTTGTTGAATTGAAATATGCCTATCAAAAATAAATTTTTCAGATTTAAAAATATGCTTATCAAAAGTAGATGGAGAGAGTATAAATTACTTTTATA

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 95.20% 4.40% 0.38% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 86.10% 12.80% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 96.00% 3.00% 1.04% 0.00% NA
Tropical Japonica  504 74.80% 24.20% 0.99% 0.00% NA
Japonica Intermediate  241 78.40% 19.90% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0317440491 C -> T LOC_Os03g30550.1 downstream_gene_variant ; 1541.0bp to feature; MODIFIER silent_mutation Average:41.415; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0317440491 C -> T LOC_Os03g30550-LOC_Os03g30570 intergenic_region ; MODIFIER silent_mutation Average:41.415; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317440491 2.80E-07 NA Grain_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