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Detailed information for vg0403478520:

Variant ID: vg0403478520 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3478520
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCGTGCCATTCAATGCTTTCAATCCTCCTCCACCGGTATGTAATCAAACATTTCAACCTTTCACAAAATATAGTTTTGTCTTTTTGTTGAATCAATTAA[C/T]
AATGAAGGATATTACACCCAGGAATTTGCTTTGATGAAGTCGGATCCCCCAGTCGTTCAACGCCGATCACCCCACCACCAAACCGGTTGAGGGAGCGGGG

Reverse complement sequence

CCCCGCTCCCTCAACCGGTTTGGTGGTGGGGTGATCGGCGTTGAACGACTGGGGGATCCGACTTCATCAAAGCAAATTCCTGGGTGTAATATCCTTCATT[G/A]
TTAATTGATTCAACAAAAAGACAAAACTATATTTTGTGAAAGGTTGAAATGTTTGATTACATACCGGTGGAGGAGGATTGAAAGCATTGAATGGCACGAC

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 61.30% 4.60% 2.05% 32.01% NA
All Indica  2759 49.50% 0.30% 1.96% 48.31% NA
All Japonica  1512 76.30% 13.80% 2.45% 7.54% NA
Aus  269 96.70% 0.00% 0.37% 2.97% NA
Indica I  595 52.30% 0.20% 2.69% 44.87% NA
Indica II  465 56.30% 0.20% 1.51% 41.94% NA
Indica III  913 40.90% 0.10% 1.53% 57.50% NA
Indica Intermediate  786 53.30% 0.50% 2.16% 44.02% NA
Temperate Japonica  767 94.50% 2.20% 0.65% 2.61% NA
Tropical Japonica  504 55.80% 29.40% 3.77% 11.11% NA
Japonica Intermediate  241 61.00% 17.80% 5.39% 15.77% NA
VI/Aromatic  96 65.60% 0.00% 1.04% 33.33% NA
Intermediate  90 64.40% 2.20% 4.44% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0403478520 C -> DEL N N silent_mutation Average:29.052; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0403478520 C -> T LOC_Os04g06610.1 downstream_gene_variant ; 2265.0bp to feature; MODIFIER silent_mutation Average:29.052; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N
vg0403478520 C -> T LOC_Os04g06600.1 intron_variant ; MODIFIER silent_mutation Average:29.052; most accessible tissue: Minghui63 panicle, score: 46.754 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403478520 8.32E-06 NA mr1083 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
vg0403478520 NA 9.30E-07 mr1155 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
vg0403478520 NA 2.67E-06 mr1213 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
vg0403478520 NA 7.07E-17 mr1301 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
vg0403478520 NA 9.84E-14 mr1410 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
vg0403478520 3.19E-07 NA mr1104_2 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
vg0403478520 4.78E-06 NA mr1107_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
vg0403478520 NA 4.91E-06 mr1155_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
vg0403478520 NA 2.65E-18 mr1301_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
vg0403478520 NA 1.11E-13 mr1410_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
vg0403478520 3.43E-08 NA mr1798_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