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Detailed information for vg1220409045:

Variant ID: vg1220409045 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20409045
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, C: 0.17, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAGGAAACAACTTTAACTTAAGCAAATCATTACTACCAACCTTACCACATTGATCAATAAATTGGCCGATATGCTCCATTTTTGTTCTAGCATCCTCA[G/C]
CTGTGAATTTCGTGAAGTTGGGCACCTCAAATCCTTGCGGGTATGGGACCGAATCTACATGTTCAGGATACGGCCTTTGATATGTATGCATAACTATTTT

Reverse complement sequence

AAAATAGTTATGCATACATATCAAAGGCCGTATCCTGAACATGTAGATTCGGTCCCATACCCGCAAGGATTTGAGGTGCCCAACTTCACGAAATTCACAG[C/G]
TGAGGATGCTAGAACAAAAATGGAGCATATCGGCCAATTTATTGATCAATGTGGTAAGGTTGGTAGTAATGATTTGCTTAAGTTAAAGTTGTTTCCTCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 29.80% 24.20% 23.85% 22.13% NA
All Indica  2759 12.40% 30.90% 27.04% 29.61% NA
All Japonica  1512 64.60% 14.00% 11.90% 9.46% NA
Aus  269 14.10% 16.00% 48.70% 21.19% NA
Indica I  595 32.60% 6.90% 23.87% 36.64% NA
Indica II  465 10.50% 38.70% 20.43% 30.32% NA
Indica III  913 1.00% 46.40% 28.59% 23.99% NA
Indica Intermediate  786 11.60% 26.50% 31.55% 30.41% NA
Temperate Japonica  767 94.30% 0.90% 2.09% 2.74% NA
Tropical Japonica  504 18.50% 35.30% 25.60% 20.63% NA
Japonica Intermediate  241 66.80% 11.20% 14.52% 7.47% NA
VI/Aromatic  96 8.30% 18.80% 53.12% 19.79% NA
Intermediate  90 45.60% 22.20% 21.11% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220409045 G -> C LOC_Os12g33840.1 downstream_gene_variant ; 3710.0bp to feature; MODIFIER silent_mutation Average:8.569; most accessible tissue: Callus, score: 19.417 N N N N
vg1220409045 G -> C LOC_Os12g33840-LOC_Os12g33870 intergenic_region ; MODIFIER silent_mutation Average:8.569; most accessible tissue: Callus, score: 19.417 N N N N
vg1220409045 G -> DEL N N silent_mutation Average:8.569; most accessible tissue: Callus, score: 19.417 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220409045 NA 2.40E-06 mr1121 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
vg1220409045 2.16E-17 1.28E-107 mr1334 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
vg1220409045 NA 1.54E-06 mr1334 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
vg1220409045 4.80E-08 8.41E-22 mr1334 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
vg1220409045 NA 1.61E-20 mr1588 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
vg1220409045 NA 4.55E-06 mr1588 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
vg1220409045 2.41E-18 6.49E-117 mr1334_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
vg1220409045 5.96E-07 3.39E-24 mr1334_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
vg1220409045 1.68E-06 1.68E-06 mr1335_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
vg1220409045 NA 1.39E-26 mr1588_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
vg1220409045 8.53E-07 3.05E-09 mr1588_2 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
vg1220409045 4.29E-06 2.90E-51 mr1991_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
vg1220409045 NA 6.32E-11 mr1991_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