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Detailed information for vg1117527349:

Variant ID: vg1117527349 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17527349
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCCGCATAAGTAAGAGGTGATTGTTTGTAGACTAAAGCCTAATATCCTGTAATAAGAACTCCAACATTGTGGTATCAGAGCTGATCTTTAGTCCACTCA[A/G]
TCCCTCATAATCACATCATCCCTGTGATTAGAAGCCATCCCTAAAAAAAGGTTCAAGATTGATTCGGCATGAACAATTTTGAATTAGATTAGATTAATTT

Reverse complement sequence

AAATTAATCTAATCTAATTCAAAATTGTTCATGCCGAATCAATCTTGAACCTTTTTTTAGGGATGGCTTCTAATCACAGGGATGATGTGATTATGAGGGA[T/C]
TGAGTGGACTAAAGATCAGCTCTGATACCACAATGTTGGAGTTCTTATTACAGGATATTAGGCTTTAGTCTACAAACAATCACCTCTTACTTATGCGGAA

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 52.10% 5.20% 1.33% 41.35% NA
All Indica  2759 38.60% 0.00% 1.70% 59.70% NA
All Japonica  1512 67.70% 15.90% 0.40% 15.94% NA
Aus  269 90.00% 0.00% 0.37% 9.67% NA
Indica I  595 32.60% 0.00% 1.34% 66.05% NA
Indica II  465 39.10% 0.20% 1.94% 58.71% NA
Indica III  913 39.90% 0.00% 1.20% 58.93% NA
Indica Intermediate  786 41.20% 0.00% 2.42% 56.36% NA
Temperate Japonica  767 67.40% 30.40% 0.13% 2.09% NA
Tropical Japonica  504 59.90% 0.40% 0.99% 38.69% NA
Japonica Intermediate  241 85.10% 2.50% 0.00% 12.45% NA
VI/Aromatic  96 78.10% 1.00% 8.33% 12.50% NA
Intermediate  90 63.30% 4.40% 1.11% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117527349 A -> DEL N N silent_mutation Average:21.071; most accessible tissue: Minghui63 root, score: 43.505 N N N N
vg1117527349 A -> G LOC_Os11g30150.1 intron_variant ; MODIFIER silent_mutation Average:21.071; most accessible tissue: Minghui63 root, score: 43.505 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117527349 NA 8.79E-10 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1117527349 NA 1.20E-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
vg1117527349 1.50E-06 1.50E-06 mr1343 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
vg1117527349 NA 2.54E-10 mr1354 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
vg1117527349 9.76E-06 NA mr1525 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
vg1117527349 1.05E-07 5.26E-11 mr1829 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
vg1117527349 NA 1.44E-09 mr1829 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
vg1117527349 NA 1.55E-06 mr1902 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
vg1117527349 NA 6.05E-07 mr1138_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
vg1117527349 3.66E-07 4.67E-09 mr1354_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
vg1117527349 NA 2.99E-13 mr1354_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
vg1117527349 NA 9.20E-06 mr1499_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
vg1117527349 NA 3.33E-06 mr1647_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
vg1117527349 8.18E-09 4.20E-14 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
vg1117527349 NA 3.84E-10 mr1829_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
vg1117527349 6.19E-07 4.41E-18 mr1902_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
vg1117527349 NA 1.36E-10 mr1902_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