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Detailed information for vg0708154795:

Variant ID: vg0708154795 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 8154795
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGTGCCAGAACTGTGTTGGCACGAACTAAGTCGACGAACACAACGGCATGGGAGATCTTCTTAGCTCCAGTGGCGGTCCAAATCTTGGTGAGATGTGGG[C/T]
GTGCCAGTCAGTTTGATCCTGCAACTGACAAGATATGTAAACAATAGATCAAATAGCCGATCGGCTGATAAGCTAATGGAGTAATTCCAGCCGATGCCGA

Reverse complement sequence

TCGGCATCGGCTGGAATTACTCCATTAGCTTATCAGCCGATCGGCTATTTGATCTATTGTTTACATATCTTGTCAGTTGCAGGATCAAACTGACTGGCAC[G/A]
CCCACATCTCACCAAGATTTGGACCGCCACTGGAGCTAAGAAGATCTCCCATGCCGTTGTGTTCGTCGACTTAGTTCGTGCCAACACAGTTCTGGCACCA

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 97.60% 1.40% 0.97% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 92.60% 4.40% 2.98% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 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 88.30% 6.30% 5.48% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 91.70% 7.50% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0708154795 C -> T LOC_Os07g14290.1 upstream_gene_variant ; 3937.0bp to feature; MODIFIER silent_mutation Average:49.062; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N
vg0708154795 C -> T LOC_Os07g14300.1 upstream_gene_variant ; 1103.0bp to feature; MODIFIER silent_mutation Average:49.062; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N
vg0708154795 C -> T LOC_Os07g14290-LOC_Os07g14300 intergenic_region ; MODIFIER silent_mutation Average:49.062; most accessible tissue: Zhenshan97 young leaf, score: 66.32 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0708154795 NA 1.52E-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
vg0708154795 NA 2.48E-07 mr1382 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
vg0708154795 3.24E-09 2.81E-10 mr1038_2 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
vg0708154795 2.42E-09 2.42E-09 mr1389_2 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