\

Search for Variation information by Variation ID:

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

Detailed information for vg0407782064:

Variant ID: vg0407782064 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7782064
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAACCCATTTTATATCAGTAATAAGTTCAATAATTTTGGTAGTCGTGGGTGGTTAGTTTTAATAGTTTGTTCTCTCTGTTGGCTGGTTTGTTTTGGGGTA[T/C]
TTCAGATGGTGATAACCAGGAGAACTGCTGCTACCGGTGATGGCAACCAACCCGAAGGTAGCAACACCAACATCCAAGGCGGCCCACCTCCACCTCCTCC

Reverse complement sequence

GGAGGAGGTGGAGGTGGGCCGCCTTGGATGTTGGTGTTGCTACCTTCGGGTTGGTTGCCATCACCGGTAGCAGCAGTTCTCCTGGTTATCACCATCTGAA[A/G]
TACCCCAAAACAAACCAGCCAACAGAGAGAACAAACTATTAAAACTAACCACCCACGACTACCAAAATTATTGAACTTATTACTGATATAAAATGGGTTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.50% 5.50% 5.23% 9.82% NA
All Indica  2759 86.20% 5.00% 7.21% 1.67% NA
All Japonica  1512 69.50% 7.60% 0.73% 22.16% NA
Aus  269 71.70% 0.70% 6.69% 20.82% NA
Indica I  595 91.80% 0.50% 6.89% 0.84% NA
Indica II  465 93.50% 3.20% 2.58% 0.65% NA
Indica III  913 76.60% 9.20% 10.73% 3.50% NA
Indica Intermediate  786 88.70% 4.50% 6.11% 0.76% NA
Temperate Japonica  767 97.00% 0.00% 0.00% 3.00% NA
Tropical Japonica  504 24.80% 21.20% 1.79% 52.18% NA
Japonica Intermediate  241 75.50% 3.30% 0.83% 20.33% NA
VI/Aromatic  96 65.60% 0.00% 12.50% 21.88% NA
Intermediate  90 80.00% 5.60% 7.78% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0407782064 T -> C LOC_Os04g13930.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:26.893; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N
vg0407782064 T -> C LOC_Os04g13920.1 upstream_gene_variant ; 4722.0bp to feature; MODIFIER silent_mutation Average:26.893; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N
vg0407782064 T -> DEL N N silent_mutation Average:26.893; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407782064 2.01E-07 NA mr1275 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
vg0407782064 1.16E-06 1.16E-06 mr1275 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
vg0407782064 NA 1.05E-06 mr1309 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
vg0407782064 NA 1.43E-07 mr1583 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
vg0407782064 2.66E-08 1.09E-07 mr1835 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
vg0407782064 5.18E-06 4.06E-07 mr1835 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
vg0407782064 NA 3.29E-07 mr1841 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
vg0407782064 1.54E-07 1.54E-07 mr1900 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
vg0407782064 NA 7.37E-07 mr1238_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
vg0407782064 NA 4.91E-06 mr1484_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
vg0407782064 NA 1.74E-07 mr1841_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
vg0407782064 NA 8.56E-07 mr1900_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