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Detailed information for vg1225594396:

Variant ID: vg1225594396 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 25594396
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.24, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAAAAAATCACAGCACACACATATGTGTAAGGATTTGTTCTCACAACCTCCATTTTACCGAAATAACATATTACAAAGAGATTTTTGAAAGTTACATA[T/C]
AAGTTACACTATAGTTACAGTGTAATTACATGTAAGTTACAGTGTAATTACACTACGATTGTACTGTAATTACATCTGTCAAATTTTTGGGAGAAAATTT

Reverse complement sequence

AAATTTTCTCCCAAAAATTTGACAGATGTAATTACAGTACAATCGTAGTGTAATTACACTGTAACTTACATGTAATTACACTGTAACTATAGTGTAACTT[A/G]
TATGTAACTTTCAAAAATCTCTTTGTAATATGTTATTTCGGTAAAATGGAGGTTGTGAGAACAAATCCTTACACATATGTGTGTGCTGTGATTTTTTTCT

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 57.40% 33.60% 0.89% 8.17% NA
All Indica  2759 39.10% 49.40% 1.05% 10.44% NA
All Japonica  1512 99.60% 0.10% 0.26% 0.07% NA
Aus  269 0.70% 68.40% 1.49% 29.37% NA
Indica I  595 85.90% 13.30% 0.34% 0.50% NA
Indica II  465 12.30% 78.90% 1.08% 7.74% NA
Indica III  913 26.00% 50.60% 1.42% 22.02% NA
Indica Intermediate  786 35.00% 57.80% 1.15% 6.11% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 0.00% NA
Japonica Intermediate  241 98.80% 0.40% 0.41% 0.41% NA
VI/Aromatic  96 72.90% 15.60% 0.00% 11.46% NA
Intermediate  90 58.90% 27.80% 5.56% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1225594396 T -> C LOC_Os12g41270.1 intron_variant ; MODIFIER silent_mutation Average:19.014; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1225594396 T -> DEL N N silent_mutation Average:19.014; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1225594396 NA 3.28E-07 mr1193 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
vg1225594396 NA 7.19E-06 mr1502 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
vg1225594396 NA 1.04E-06 mr1709 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
vg1225594396 NA 3.08E-07 mr1931 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
vg1225594396 NA 1.38E-07 mr1057_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
vg1225594396 NA 5.94E-10 mr1170_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
vg1225594396 NA 1.36E-07 mr1184_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
vg1225594396 NA 2.56E-07 mr1278_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
vg1225594396 NA 4.97E-06 mr1293_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
vg1225594396 NA 2.42E-07 mr1329_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
vg1225594396 NA 1.05E-06 mr1508_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
vg1225594396 NA 6.88E-07 mr1524_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
vg1225594396 NA 1.00E-08 mr1683_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
vg1225594396 NA 5.68E-06 mr1733_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
vg1225594396 NA 2.19E-06 mr1745_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
vg1225594396 NA 9.50E-06 mr1843_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
vg1225594396 NA 6.68E-07 mr1904_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
vg1225594396 NA 1.65E-06 mr1982_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