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Detailed information for vg0118901136:

Variant ID: vg0118901136 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18901136
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGTGTGTGAGAGTTTGGTTGGCCTGATGTTGAATATTCCCGGGAAGACAAAGGACGGGTTGAACGCGCGCCTTGATCTACAGGACATGAATATTTGCAG[C/T]
GAACTCTAGCCCATACGAGATGCAGAGACAGGTAAAGTGTACCTCCCTCCAGCCTGCCACACACTGTCGAAGGATGAGAAGATCGCAATGTTATCATGCT

Reverse complement sequence

AGCATGATAACATTGCGATCTTCTCATCCTTCGACAGTGTGTGGCAGGCTGGAGGGAGGTACACTTTACCTGTCTCTGCATCTCGTATGGGCTAGAGTTC[G/A]
CTGCAAATATTCATGTCCTGTAGATCAAGGCGCGCGTTCAACCCGTCCTTTGTCTTCCCGGGAATATTCAACATCAGGCCAACCAAACTCTCACACACAT

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 41.20% 0.30% 14.49% 44.01% NA
All Indica  2759 7.90% 0.40% 19.54% 72.09% NA
All Japonica  1512 94.80% 0.00% 2.98% 2.18% NA
Aus  269 52.80% 0.00% 33.46% 13.75% NA
Indica I  595 2.50% 0.30% 24.71% 72.44% NA
Indica II  465 6.50% 0.20% 27.96% 65.38% NA
Indica III  913 10.30% 0.00% 9.64% 80.07% NA
Indica Intermediate  786 10.20% 1.10% 22.14% 66.54% NA
Temperate Japonica  767 99.20% 0.00% 0.00% 0.78% NA
Tropical Japonica  504 86.50% 0.00% 8.73% 4.76% NA
Japonica Intermediate  241 98.30% 0.00% 0.41% 1.24% NA
VI/Aromatic  96 97.90% 0.00% 1.04% 1.04% NA
Intermediate  90 66.70% 0.00% 11.11% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0118901136 C -> T LOC_Os01g34290.1 missense_variant&splice_region_variant ; p.Ala339Val; MODERATE nonsynonymous_codon ; A339V Average:12.633; most accessible tissue: Callus, score: 17.978 unknown unknown TOLERATED 0.16
vg0118901136 C -> DEL LOC_Os01g34290.1 N frameshift_variant Average:12.633; most accessible tissue: Callus, score: 17.978 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118901136 NA 4.72E-15 mr1164 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
vg0118901136 NA 7.74E-07 mr1220 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
vg0118901136 NA 3.77E-16 mr1228 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
vg0118901136 NA 1.81E-06 mr1315 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
vg0118901136 NA 2.09E-06 mr1392 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
vg0118901136 NA 5.91E-08 mr1506 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
vg0118901136 NA 2.42E-07 mr1604 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
vg0118901136 NA 2.57E-06 mr1622 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
vg0118901136 NA 1.44E-08 mr1776 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
vg0118901136 NA 1.12E-07 mr1824 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
vg0118901136 NA 4.29E-06 mr1881 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
vg0118901136 1.77E-06 1.83E-26 mr1943 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