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Detailed information for vg0401042995:

Variant ID: vg0401042995 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1042995
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCGATGTCTTCTTCGCCATCGACATTGCCATATCCTTCTTCGTCACGTACCGTGACACCTCCACTTGCCTCCTCATAACTGACCGCAGGAAGATCACAA[C/A]
TAGGTGATGATCCCTCACTCTATGCTACTCACACGTGCCTCTCCATGGATTTTCTTTTTGTTTCTGTTAGAGTTCTGATTTGTTAATATGCACGGACTGA

Reverse complement sequence

TCAGTCCGTGCATATTAACAAATCAGAACTCTAACAGAAACAAAAAGAAAATCCATGGAGAGGCACGTGTGAGTAGCATAGAGTGAGGGATCATCACCTA[G/T]
TTGTGATCTTCCTGCGGTCAGTTATGAGGAGGCAAGTGGAGGTGTCACGGTACGTGACGAAGAAGGATATGGCAATGTCGATGGCGAAGAAGACATCGAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.10% 6.90% 0.02% 0.00% NA
All Indica  2759 98.60% 1.40% 0.04% 0.00% NA
All Japonica  1512 91.10% 8.90% 0.00% 0.00% NA
Aus  269 61.30% 38.70% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.50% 0.13% 0.00% NA
Temperate Japonica  767 93.90% 6.10% 0.00% 0.00% NA
Tropical Japonica  504 93.50% 6.50% 0.00% 0.00% NA
Japonica Intermediate  241 77.60% 22.40% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 47.90% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0401042995 C -> A LOC_Os04g02710.1 upstream_gene_variant ; 3118.0bp to feature; MODIFIER silent_mutation Average:36.613; most accessible tissue: Callus, score: 64.16 N N N N
vg0401042995 C -> A LOC_Os04g02730.1 upstream_gene_variant ; 3907.0bp to feature; MODIFIER silent_mutation Average:36.613; most accessible tissue: Callus, score: 64.16 N N N N
vg0401042995 C -> A LOC_Os04g02720.1 intron_variant ; MODIFIER silent_mutation Average:36.613; most accessible tissue: Callus, score: 64.16 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401042995 7.62E-07 NA mr1274 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
vg0401042995 NA 6.76E-06 mr1829_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