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Detailed information for vg0607152342:

Variant ID: vg0607152342 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7152342
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCTTTAATATTGAGAATGTCACATTTTTAAGTGCTCACGTTTTTTAAACATCCACTCAGCATTTCAACTTTAAATTTGAGAAGAAAGTCAATATAGTA[C/T]
GAAACCATCAGAAAGAAGTAGGAGAGAAATTTGGTTGCATGTGATATCATTCATACAAAAAAGTACTTACCCCATCAGTAATCCAATATAAATATTGTAT

Reverse complement sequence

ATACAATATTTATATTGGATTACTGATGGGGTAAGTACTTTTTTGTATGAATGATATCACATGCAACCAAATTTCTCTCCTACTTCTTTCTGATGGTTTC[G/A]
TACTATATTGACTTTCTTCTCAAATTTAAAGTTGAAATGCTGAGTGGATGTTTAAAAAACGTGAGCACTTAAAAATGTGACATTCTCAATATTAAAGGAT

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 78.20% 20.10% 1.63% 0.00% NA
All Indica  2759 92.40% 7.60% 0.04% 0.00% NA
All Japonica  1512 47.90% 47.20% 4.83% 0.00% NA
Aus  269 95.90% 3.70% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 88.20% 11.80% 0.00% 0.00% NA
Indica Intermediate  786 88.70% 11.20% 0.13% 0.00% NA
Temperate Japonica  767 61.80% 30.80% 7.43% 0.00% NA
Tropical Japonica  504 27.20% 70.40% 2.38% 0.00% NA
Japonica Intermediate  241 47.30% 51.00% 1.66% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 80.00% 17.80% 2.22% 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
vg0607152342 C -> T LOC_Os06g13050.1 intron_variant ; MODIFIER silent_mutation Average:35.388; most accessible tissue: Callus, score: 49.481 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607152342 NA 4.54E-06 mr1002 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
vg0607152342 NA 8.29E-06 mr1180 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
vg0607152342 NA 8.38E-07 mr1183 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
vg0607152342 NA 1.34E-08 mr1354 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
vg0607152342 NA 5.17E-07 mr1408 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
vg0607152342 NA 6.27E-07 mr1503 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
vg0607152342 NA 3.95E-09 mr1794 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
vg0607152342 NA 1.53E-06 mr1183_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
vg0607152342 NA 9.49E-11 mr1794_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