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Detailed information for vg1118531424:

Variant ID: vg1118531424 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18531424
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACACTCACAACGTTTCACTATATATAGATCTAATGTTGCAGTGAACTAAAATATTCCATTGCAACAAATCACCCACATATTTTAGAAATCCTCTGTTAAG[G/A]
AAATTTGTTTTATTTTTTGTTCCACAAAAAATATTTCACCTAATGTACTTACAATGTTTTACAATGTTTCACTATGTATGGATCAAATGTTGCAGTGAAC

Reverse complement sequence

GTTCACTGCAACATTTGATCCATACATAGTGAAACATTGTAAAACATTGTAAGTACATTAGGTGAAATATTTTTTGTGGAACAAAAAATAAAACAAATTT[C/T]
CTTAACAGAGGATTTCTAAAATATGTGGGTGATTTGTTGCAATGGAATATTTTAGTTCACTGCAACATTAGATCTATATATAGTGAAACGTTGTGAGTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 4.00% 0.53% 1.69% NA
All Indica  2759 96.80% 0.80% 0.40% 1.96% NA
All Japonica  1512 98.30% 0.30% 0.26% 1.19% NA
Aus  269 42.40% 55.80% 1.49% 0.37% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 98.70% 0.40% 0.43% 0.43% NA
Indica III  913 93.90% 1.30% 0.66% 4.16% NA
Indica Intermediate  786 97.10% 0.90% 0.25% 1.78% NA
Temperate Japonica  767 97.70% 0.00% 0.00% 2.35% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 1.70% 1.66% 0.00% NA
VI/Aromatic  96 77.10% 10.40% 5.21% 7.29% NA
Intermediate  90 95.60% 3.30% 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
vg1118531424 G -> A LOC_Os11g31680.1 intron_variant ; MODIFIER silent_mutation Average:39.867; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg1118531424 G -> DEL N N silent_mutation Average:39.867; 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
vg1118531424 3.18E-06 2.70E-17 mr1113 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
vg1118531424 4.66E-08 1.16E-20 mr1114 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
vg1118531424 1.70E-06 NA mr1116 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
vg1118531424 7.15E-07 NA mr1242 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
vg1118531424 NA 1.72E-06 mr1417 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
vg1118531424 1.26E-06 NA mr1113_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
vg1118531424 1.70E-07 NA mr1114_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
vg1118531424 2.68E-06 NA mr1118_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
vg1118531424 9.34E-08 8.63E-19 mr1240_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
vg1118531424 4.91E-07 NA mr1242_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
vg1118531424 7.57E-06 NA mr1247_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