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Detailed information for vg0304064339:

Variant ID: vg0304064339 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 4064339
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATGACAGAGTGGGTCAGGTTGGTAGGAGGCGTCACAAGAGGCCGGTTGGGCTGTGTTTGGATCAAAGAATTGAGGATTTAGGTGCACTAATATGTGTA[C/T]
ATGTGTATATACTAGAAGCATACTTGTTTTTTTTTTATAAAAATGTTGGGTATTCCCGAGAATATCCAGGAATCATGGTAGCTCCGCCCCTTACGTGTAC

Reverse complement sequence

GTACACGTAAGGGGCGGAGCTACCATGATTCCTGGATATTCTCGGGAATACCCAACATTTTTATAAAAAAAAAACAAGTATGCTTCTAGTATATACACAT[G/A]
TACACATATTAGTGCACCTAAATCCTCAATTCTTTGATCCAAACACAGCCCAACCGGCCTCTTGTGACGCCTCCTACCAACCTGACCCACTCTGTCATGA

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 97.00% 2.90% 0.08% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 95.20% 4.50% 0.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 93.50% 6.10% 0.39% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 5.80% 0.41% 0.00% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0304064339 C -> T LOC_Os03g07940.1 upstream_gene_variant ; 2872.0bp to feature; MODIFIER silent_mutation Average:70.008; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0304064339 C -> T LOC_Os03g07950.1 upstream_gene_variant ; 1820.0bp to feature; MODIFIER silent_mutation Average:70.008; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N
vg0304064339 C -> T LOC_Os03g07940-LOC_Os03g07950 intergenic_region ; MODIFIER silent_mutation Average:70.008; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0304064339 NA 1.05E-06 mr1380_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
vg0304064339 NA 1.12E-06 mr1561_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
vg0304064339 9.10E-08 9.09E-08 mr1908_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
vg0304064339 NA 1.80E-07 mr1996_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