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Detailed information for vg0117060548:

Variant ID: vg0117060548 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 17060548
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


CTGATAATTAAGTTCACGAGCTCGAGCTCTAGTCATTGGTCCTTGCTGTGTAATAGGCGTGGTTGTATCGTTGGAAGGGATGTCCTCATCATCCACCATG[T/C]
GCGCCAGGTGCATGATGGTAGCGTCATCCTCCGAGCTAGCATCCCGGAAGGTGGCGTAGTCGCGGGCTCCTCCGCGACGAGGGTGGTAGCGGTAGGGCAA

Reverse complement sequence

TTGCCCTACCGCTACCACCCTCGTCGCGGAGGAGCCCGCGACTACGCCACCTTCCGGGATGCTAGCTCGGAGGATGACGCTACCATCATGCACCTGGCGC[A/G]
CATGGTGGATGATGAGGACATCCCTTCCAACGATACAACCACGCCTATTACACAGCAAGGACCAATGACTAGAGCTCGAGCTCGTGAACTTAATTATCAG

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 25.50% 12.20% 30.91% 31.40% NA
All Indica  2759 3.00% 3.10% 44.04% 49.91% NA
All Japonica  1512 60.10% 31.80% 5.89% 2.25% NA
Aus  269 32.00% 0.40% 47.58% 20.07% NA
Indica I  595 1.50% 1.80% 35.46% 61.18% NA
Indica II  465 4.90% 1.50% 47.53% 46.02% NA
Indica III  913 1.10% 3.60% 48.63% 46.66% NA
Indica Intermediate  786 5.10% 4.30% 43.13% 47.46% NA
Temperate Japonica  767 39.10% 51.50% 8.47% 0.91% NA
Tropical Japonica  504 91.70% 1.60% 2.18% 4.56% NA
Japonica Intermediate  241 60.60% 32.40% 5.39% 1.66% NA
VI/Aromatic  96 93.80% 0.00% 5.21% 1.04% NA
Intermediate  90 44.40% 8.90% 26.67% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0117060548 T -> DEL LOC_Os01g31200.1 N frameshift_variant Average:16.8; most accessible tissue: Callus, score: 37.276 N N N N
vg0117060548 T -> C LOC_Os01g31200.1 missense_variant ; p.His189Arg; MODERATE nonsynonymous_codon ; H189R Average:16.8; most accessible tissue: Callus, score: 37.276 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0117060548 NA 3.08E-06 mr1077 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
vg0117060548 NA 1.07E-10 mr1084 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
vg0117060548 NA 5.37E-18 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
vg0117060548 NA 1.89E-06 mr1164 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
vg0117060548 7.42E-06 8.29E-07 mr1170 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
vg0117060548 NA 4.85E-07 mr1202 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
vg0117060548 NA 2.78E-12 mr1205 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
vg0117060548 4.96E-06 NA mr1318 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
vg0117060548 NA 4.94E-07 mr1338 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
vg0117060548 NA 7.37E-07 mr1359 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
vg0117060548 NA 5.39E-07 mr1548 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
vg0117060548 NA 1.93E-06 mr1576 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
vg0117060548 NA 7.25E-20 mr1627 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
vg0117060548 NA 4.42E-08 mr1627 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
vg0117060548 NA 1.86E-07 mr1680 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
vg0117060548 NA 3.75E-06 mr1729 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
vg0117060548 NA 5.55E-08 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
vg0117060548 NA 4.46E-19 mr1825 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
vg0117060548 NA 4.30E-07 mr1851 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