\

Search for Variation information by Variation ID:

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

Detailed information for vg1105599945:

Variant ID: vg1105599945 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 5599945
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACATGATTTCTTAACAAAATAAGTCTACTTTCTTTCTCGATAACTGGATGGATAATTACTCATAGGGATGAATTAAATATTTTGTTGTATAAAACTAACA[A/G]
ATAGCTTATAAAAATTATCAAAGAATATCGTTGAAAAACAATCGTAGAGAAATACTTTTTTGAAATTTGAAGCGTAGCATATACTGTCTGGTTAATATTC

Reverse complement sequence

GAATATTAACCAGACAGTATATGCTACGCTTCAAATTTCAAAAAAGTATTTCTCTACGATTGTTTTTCAACGATATTCTTTGATAATTTTTATAAGCTAT[T/C]
TGTTAGTTTTATACAACAAAATATTTAATTCATCCCTATGAGTAATTATCCATCCAGTTATCGAGAAAGAAAGTAGACTTATTTTGTTAAGAAATCATGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.70% 7.40% 2.45% 3.45% NA
All Indica  2759 91.50% 6.70% 1.74% 0.04% NA
All Japonica  1512 89.30% 0.10% 0.20% 10.38% NA
Aus  269 19.70% 56.50% 23.42% 0.37% NA
Indica I  595 73.80% 21.30% 4.87% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.90% 2.20% 0.88% 0.00% NA
Indica Intermediate  786 93.60% 4.80% 1.40% 0.13% NA
Temperate Japonica  767 91.50% 0.00% 0.39% 8.08% NA
Tropical Japonica  504 93.10% 0.20% 0.00% 6.75% NA
Japonica Intermediate  241 74.30% 0.40% 0.00% 25.31% NA
VI/Aromatic  96 94.80% 1.00% 1.04% 3.12% NA
Intermediate  90 90.00% 7.80% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105599945 A -> DEL N N silent_mutation Average:29.871; most accessible tissue: Zhenshan97 root, score: 54.262 N N N N
vg1105599945 A -> G LOC_Os11g10310.1 intron_variant ; MODIFIER silent_mutation Average:29.871; most accessible tissue: Zhenshan97 root, score: 54.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105599945 NA 6.63E-10 mr1004 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
vg1105599945 NA 2.59E-09 mr1005 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
vg1105599945 NA 4.31E-08 mr1006 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
vg1105599945 NA 2.94E-06 mr1007 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
vg1105599945 NA 4.71E-08 mr1052 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
vg1105599945 NA 2.74E-07 mr1343 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
vg1105599945 NA 6.21E-07 mr1758 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
vg1105599945 NA 9.85E-14 mr1918 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
vg1105599945 NA 9.52E-06 mr1236_2 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
vg1105599945 NA 2.70E-08 mr1378_2 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
vg1105599945 NA 4.18E-10 mr1758_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
vg1105599945 NA 1.45E-08 mr1829_2 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