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Detailed information for vg1015968448:

Variant ID: vg1015968448 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15968448
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTAAATAATCTATCATTAGCAAATGTTTACTGCAGCACCACATTGTCAAATCATGAAGCAATTAGGCTTGAAAGATTCGTCTCGCAATTTACATACAAT[A/C]
TGTATAATTAGTTATTTTTTATATTATTTAATACTCCATGCATACGTCCAAACATTCGATGTGACAGGGTAAAAAAATTTTGCCCGGGGATCTAAACAGG

Reverse complement sequence

CCTGTTTAGATCCCCGGGCAAAATTTTTTTACCCTGTCACATCGAATGTTTGGACGTATGCATGGAGTATTAAATAATATAAAAAATAACTAATTATACA[T/G]
ATTGTATGTAAATTGCGAGACGAATCTTTCAAGCCTAATTGCTTCATGATTTGACAATGTGGTGCTGCAGTAAACATTTGCTAATGATAGATTATTTAGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 6.30% 0.02% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 81.00% 19.00% 0.00% 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 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 90.90% 9.10% 0.00% 0.00% NA
Tropical Japonica  504 81.90% 18.10% 0.00% 0.00% NA
Japonica Intermediate  241 47.70% 52.30% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 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
vg1015968448 A -> C LOC_Os10g30660.1 upstream_gene_variant ; 3697.0bp to feature; MODIFIER silent_mutation Average:53.396; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg1015968448 A -> C LOC_Os10g30670.1 upstream_gene_variant ; 225.0bp to feature; MODIFIER silent_mutation Average:53.396; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg1015968448 A -> C LOC_Os10g30660-LOC_Os10g30670 intergenic_region ; MODIFIER silent_mutation Average:53.396; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015968448 NA 1.91E-06 mr1534 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
vg1015968448 3.30E-09 NA mr1745 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
vg1015968448 NA 1.35E-07 mr1745 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
vg1015968448 9.85E-08 NA mr1745_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
vg1015968448 NA 1.22E-07 mr1745_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