Search for Variation information by Variation ID:

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

Detailed information for vg0619257211:

Variant ID: vg0619257211 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19257211
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCCAACTCACCCTAGGCTAGCGGAGACCAACACCTCTGACGGCCTTCTAGTAACTTGCCCGTCAGAGGTGGATGTCACCTGTGACGGCCGGCCACCCGT[T/C]
AAAGGTGACTGGACTCACCAGTGACCACTGATCACTGACCATGCGTGAAGCCGTCAAAGATGATGGTTTGGGTCCGTGACAGGTGACCTTGGCCAGTGTA

Reverse complement sequence

TACACTGGCCAAGGTCACCTGTCACGGACCCAAACCATCATCTTTGACGGCTTCACGCATGGTCAGTGATCAGTGGTCACTGGTGAGTCCAGTCACCTTT[A/G]
ACGGGTGGCCGGCCGTCACAGGTGACATCCACCTCTGACGGGCAAGTTACTAGAAGGCCGTCAGAGGTGTTGGTCTCCGCTAGCCTAGGGTGAGTTGGGA

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 67.40% 26.10% 0.21% 6.22% NA
All Indica  2759 96.60% 3.00% 0.07% 0.36% NA
All Japonica  1512 6.60% 74.40% 0.46% 18.52% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.80% 2.70% 0.17% 1.34% NA
Indica II  465 95.50% 4.30% 0.22% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 94.90% 4.80% 0.00% 0.25% NA
Temperate Japonica  767 3.70% 67.70% 0.91% 27.77% NA
Tropical Japonica  504 11.70% 84.90% 0.00% 3.37% NA
Japonica Intermediate  241 5.40% 73.90% 0.00% 20.75% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 64.40% 31.10% 1.11% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619257211 T -> C LOC_Os06g33080.1 downstream_gene_variant ; 935.0bp to feature; MODIFIER silent_mutation Average:56.08; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0619257211 T -> C LOC_Os06g33070.1 intron_variant ; MODIFIER silent_mutation Average:56.08; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N
vg0619257211 T -> DEL N N silent_mutation Average:56.08; most accessible tissue: Zhenshan97 panicle, score: 71.253 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619257211 2.56E-09 3.04E-76 mr1033 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
vg0619257211 1.03E-06 NA mr1033 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
vg0619257211 NA 1.47E-76 mr1100 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
vg0619257211 NA 4.69E-36 mr1105 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
vg0619257211 NA 6.04E-91 mr1140 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
vg0619257211 9.16E-06 3.85E-40 mr1176 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
vg0619257211 NA 6.80E-26 mr1223 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
vg0619257211 NA 8.62E-89 mr1395 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
vg0619257211 NA 5.04E-27 mr1423 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
vg0619257211 NA 1.13E-17 mr1529 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
vg0619257211 9.83E-06 NA mr1536 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
vg0619257211 NA 6.40E-29 mr1546 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
vg0619257211 NA 1.64E-65 mr1619 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
vg0619257211 NA 5.77E-06 mr1925 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
vg0619257211 4.21E-10 3.48E-104 mr1033_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
vg0619257211 4.38E-06 NA mr1536_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