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Detailed information for vg1005203428:

Variant ID: vg1005203428 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5203428
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTAATATTGTTATACTCCCTCCATATTTTAATGTATGACGCCGTTAACTTTTTAACCAACGTTTGACCATTCATCTTATTCAAAAATTTTATGCAAATA[T/C]
AAAAATACTTATGTCATGCTTAAAGAGCATTTGATGATAAATCAAGTCACAATAAAATAAATTATAATTACATAAAATTTTTGAATAAAACGAAAGGTCA

Reverse complement sequence

TGACCTTTCGTTTTATTCAAAAATTTTATGTAATTATAATTTATTTTATTGTGACTTGATTTATCATCAAATGCTCTTTAAGCATGACATAAGTATTTTT[A/G]
TATTTGCATAAAATTTTTGAATAAGATGAATGGTCAAACGTTGGTTAAAAAGTTAACGGCGTCATACATTAAAATATGGAGGGAGTATAACAATATTACA

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 33.30% 0.40% 1.65% 64.62% NA
All Indica  2759 12.00% 0.70% 0.94% 86.34% NA
All Japonica  1512 76.70% 0.00% 3.11% 20.24% NA
Aus  269 0.70% 0.40% 0.00% 98.88% NA
Indica I  595 3.20% 1.30% 0.00% 95.46% NA
Indica II  465 16.30% 0.20% 0.86% 82.58% NA
Indica III  913 17.60% 0.90% 1.53% 79.96% NA
Indica Intermediate  786 9.70% 0.30% 1.02% 89.06% NA
Temperate Japonica  767 80.20% 0.00% 0.13% 19.69% NA
Tropical Japonica  504 70.80% 0.00% 8.93% 20.24% NA
Japonica Intermediate  241 77.60% 0.00% 0.41% 21.99% NA
VI/Aromatic  96 46.90% 0.00% 3.12% 50.00% NA
Intermediate  90 40.00% 0.00% 2.22% 57.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005203428 T -> C LOC_Os10g09620.1 intron_variant ; MODIFIER silent_mutation Average:47.331; most accessible tissue: Minghui63 root, score: 73.351 N N N N
vg1005203428 T -> DEL N N silent_mutation Average:47.331; most accessible tissue: Minghui63 root, score: 73.351 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005203428 NA 8.59E-08 mr1278 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
vg1005203428 NA 7.80E-06 mr1608 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
vg1005203428 8.24E-06 NA mr1758 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
vg1005203428 2.76E-06 2.76E-06 mr1758 Jap_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
vg1005203428 NA 1.47E-06 mr1379_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
vg1005203428 NA 9.40E-08 mr1399_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
vg1005203428 NA 4.89E-07 mr1401_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
vg1005203428 NA 3.08E-06 mr1860_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