Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0717420887:

Variant ID: vg0717420887 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 17420887
Reference Allele: GTAlternative Allele: AT,G
Primary Allele: GTSecondary Allele: AT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCGGATTGTACATCAGATAAGTAATTTGAGAGGAAACTTTATTTGAATAGGAAAAAGACACCCACGTGAACTTTATTTGAAAGGAAAAAGACACCCAT[GT/AT,G]
GGATGGACATCATAGCGACGTGCACAGTTAGACGGCTCTGAGATGCGTCGCGCTGTAGAGCTAAACCGAGAGCGTTCTCGAAATAGATTTCGCGTTGTCT

Reverse complement sequence

AGACAACGCGAAATCTATTTCGAGAACGCTCTCGGTTTAGCTCTACAGCGCGACGCATCTCAGAGCCGTCTAACTGTGCACGTCGCTATGATGTCCATCC[AC/AT,C]
ATGGGTGTCTTTTTCCTTTCAAATAAAGTTCACGTGGGTGTCTTTTTCCTATTCAAATAAAGTTTCCTCTCAAATTACTTATCTGATGTACAATCCGATT

Allele Frequencies:

Populations Population SizeFrequency of GT(primary allele) Frequency of AT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.30% 19.40% 0.19% 0.00% G: 0.02%
All Indica  2759 71.90% 27.70% 0.33% 0.00% G: 0.04%
All Japonica  1512 93.10% 6.90% 0.00% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 83.20% 16.50% 0.34% 0.00% NA
Indica II  465 36.10% 63.90% 0.00% 0.00% NA
Indica III  913 84.80% 14.70% 0.44% 0.00% G: 0.11%
Indica Intermediate  786 69.60% 30.00% 0.38% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 88.30% 11.70% 0.00% 0.00% NA
Japonica Intermediate  241 84.60% 15.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0717420887 GT -> G LOC_Os07g29630.1 downstream_gene_variant ; 413.0bp to feature; MODIFIER N Average:67.06; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0717420887 GT -> G LOC_Os07g29620-LOC_Os07g29630 intergenic_region ; MODIFIER N Average:67.06; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0717420887 GT -> AT LOC_Os07g29630.1 downstream_gene_variant ; 414.0bp to feature; MODIFIER silent_mutation Average:67.06; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0717420887 GT -> AT LOC_Os07g29620-LOC_Os07g29630 intergenic_region ; MODIFIER silent_mutation Average:67.06; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717420887 NA 3.23E-09 mr1707 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
vg0717420887 NA 1.84E-06 mr1728 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
vg0717420887 2.68E-08 2.02E-12 mr1707_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
vg0717420887 1.74E-06 1.42E-08 mr1707_2 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
vg0717420887 NA 9.22E-06 mr1728_2 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