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Detailed information for vg0630642055:

Variant ID: vg0630642055 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 30642055
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.12, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


GCTGTGCTCGCGGTTAATGAGCGCCGAGACCTGTACTACTCTTGACTAGACTTATAGATTTTAATACTGCTTAGAGTAGTTATGAGAGACATGTGAACCT[C/T]
GCCCATAGAGTGGGAAGGTCAGTATAGTAGAGTTAATAAGACGAAATATGAGGGTAAACCGAACTAAGCAGGGCTTGGAGAGGTGGATGAAACCTAAATA

Reverse complement sequence

TATTTAGGTTTCATCCACCTCTCCAAGCCCTGCTTAGTTCGGTTTACCCTCATATTTCGTCTTATTAACTCTACTATACTGACCTTCCCACTCTATGGGC[G/A]
AGGTTCACATGTCTCTCATAACTACTCTAAGCAGTATTAAAATCTATAAGTCTAGTCAAGAGTAGTACAGGTCTCGGCGCTCATTAACCGCGAGCACAGC

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 37.10% 17.10% 4.49% 41.26% NA
All Indica  2759 55.10% 0.90% 7.18% 36.79% NA
All Japonica  1512 12.90% 51.00% 0.33% 35.78% NA
Aus  269 1.10% 0.00% 0.74% 98.14% NA
Indica I  595 80.30% 1.00% 14.29% 4.37% NA
Indica II  465 57.60% 1.70% 5.38% 35.27% NA
Indica III  913 36.40% 0.30% 1.53% 61.77% NA
Indica Intermediate  786 56.20% 1.10% 9.41% 33.21% NA
Temperate Japonica  767 5.70% 83.10% 0.39% 10.82% NA
Tropical Japonica  504 24.00% 4.20% 0.00% 71.83% NA
Japonica Intermediate  241 12.40% 46.90% 0.83% 39.83% NA
VI/Aromatic  96 3.10% 0.00% 2.08% 94.79% NA
Intermediate  90 37.80% 13.30% 5.56% 43.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0630642055 C -> T LOC_Os06g50620.1 upstream_gene_variant ; 2302.0bp to feature; MODIFIER silent_mutation Average:29.869; most accessible tissue: Minghui63 root, score: 45.031 N N N N
vg0630642055 C -> T LOC_Os06g50630.1 downstream_gene_variant ; 3030.0bp to feature; MODIFIER silent_mutation Average:29.869; most accessible tissue: Minghui63 root, score: 45.031 N N N N
vg0630642055 C -> T LOC_Os06g50620-LOC_Os06g50630 intergenic_region ; MODIFIER silent_mutation Average:29.869; most accessible tissue: Minghui63 root, score: 45.031 N N N N
vg0630642055 C -> DEL N N silent_mutation Average:29.869; most accessible tissue: Minghui63 root, score: 45.031 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0630642055 NA 1.19E-17 mr1308 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
vg0630642055 NA 1.23E-07 mr1308 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
vg0630642055 NA 9.16E-09 mr1364 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
vg0630642055 NA 2.10E-06 mr1364 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
vg0630642055 NA 1.09E-10 mr1368 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
vg0630642055 NA 3.68E-08 mr1443 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
vg0630642055 NA 1.06E-06 mr1443 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
vg0630642055 NA 1.58E-11 mr1471 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
vg0630642055 NA 2.40E-06 mr1471 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
vg0630642055 NA 1.97E-07 mr1543 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
vg0630642055 NA 5.79E-09 mr1593 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
vg0630642055 NA 6.56E-06 mr1648 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
vg0630642055 1.12E-06 1.57E-17 mr1653 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
vg0630642055 NA 4.95E-06 mr1653 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
vg0630642055 NA 1.19E-08 mr1815 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
vg0630642055 NA 2.30E-13 mr1879 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
vg0630642055 NA 7.01E-07 mr1047_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
vg0630642055 NA 1.59E-07 mr1268_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
vg0630642055 NA 6.10E-06 mr1449_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
vg0630642055 NA 6.70E-09 mr1471_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
vg0630642055 NA 3.35E-09 mr1543_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
vg0630642055 NA 2.61E-11 mr1879_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