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Detailed information for vg0405234320:

Variant ID: vg0405234320 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5234320
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAATTGTTCGAATGAAGCATTTTTAAATTCACGACCATTATCACTTCGAATTCTTTTCAAAGAACCAGGAAATTCAACCTCCAATCGAAGAAACAAAC[C/T]
ACAAAAGTGTTGAAAAGCTTCATCCTTAGTTGCCATAAAGAAAACCCAAGAATATCGAGAAAAATCGACAACAATAACCAACACATACCACTTTCCTCCA

Reverse complement sequence

TGGAGGAAAGTGGTATGTGTTGGTTATTGTTGTCGATTTTTCTCGATATTCTTGGGTTTTCTTTATGGCAACTAAGGATGAAGCTTTTCAACACTTTTGT[G/A]
GTTTGTTTCTTCGATTGGAGGTTGAATTTCCTGGTTCTTTGAAAAGAATTCGAAGTGATAATGGTCGTGAATTTAAAAATGCTTCATTCGAACAATTTTG

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 82.90% 8.60% 5.97% 2.54% NA
All Indica  2759 88.80% 1.70% 6.92% 2.50% NA
All Japonica  1512 70.40% 22.80% 3.84% 2.91% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 76.60% 3.40% 15.46% 4.54% NA
Indica II  465 88.60% 0.90% 8.17% 2.37% NA
Indica III  913 98.20% 0.70% 0.66% 0.44% NA
Indica Intermediate  786 87.30% 2.30% 7.00% 3.44% NA
Temperate Japonica  767 93.60% 1.70% 3.65% 1.04% NA
Tropical Japonica  504 31.90% 56.70% 4.56% 6.75% NA
Japonica Intermediate  241 77.20% 19.10% 2.90% 0.83% NA
VI/Aromatic  96 63.50% 6.20% 29.17% 1.04% NA
Intermediate  90 80.00% 10.00% 5.56% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405234320 C -> DEL N N silent_mutation Average:12.137; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N
vg0405234320 C -> T LOC_Os04g09750-LOC_Os04g09770 intergenic_region ; MODIFIER silent_mutation Average:12.137; most accessible tissue: Minghui63 panicle, score: 29.741 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405234320 NA 5.86E-07 mr1554 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
vg0405234320 8.82E-07 NA mr1136_2 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
vg0405234320 NA 5.68E-08 mr1364_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
vg0405234320 NA 6.87E-07 mr1554_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
vg0405234320 NA 1.56E-06 mr1606_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
vg0405234320 NA 4.98E-09 mr1696_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
vg0405234320 NA 2.22E-07 mr1696_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
vg0405234320 NA 4.87E-07 mr1819_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
vg0405234320 NA 2.20E-07 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
vg0405234320 NA 1.33E-08 mr1905_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