Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0712977464:

Variant ID: vg0712977464 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 12977464
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGACATATGGGCCCTCCAATCAGTGTAAACACGTCCGGAATGTGCAAAGGTTCATTTTGTCGCATGACGAGTCTGTTTTCTCCTTAAAATACCTGCATA[C/A,T]
ACATATTTCACCAACACTAGTGGAAATGATTAGTAATAATCCCTACCACTAAGTTGGATACCATATTTTAGTTCATTATATGAAGGTATTGACAGTCAGA

Reverse complement sequence

TCTGACTGTCAATACCTTCATATAATGAACTAAAATATGGTATCCAACTTAGTGGTAGGGATTATTACTAATCATTTCCACTAGTGTTGGTGAAATATGT[G/T,A]
TATGCAGGTATTTTAAGGAGAAAACAGACTCGTCATGCGACAAAATGAACCTTTGCACATTCCGGACGTGTTTACACTGATTGGAGGGCCCATATGTCAA

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 76.90% 0.10% 0.70% 22.24% T: 0.04%
All Indica  2759 71.80% 0.30% 1.12% 26.79% NA
All Japonica  1512 87.30% 0.00% 0.07% 12.50% T: 0.13%
Aus  269 72.90% 0.00% 0.00% 27.14% NA
Indica I  595 85.70% 0.00% 1.51% 12.77% NA
Indica II  465 74.80% 0.00% 0.43% 24.73% NA
Indica III  913 59.60% 0.40% 1.20% 38.77% NA
Indica Intermediate  786 73.80% 0.40% 1.15% 24.68% NA
Temperate Japonica  767 85.40% 0.00% 0.13% 14.21% T: 0.26%
Tropical Japonica  504 90.90% 0.00% 0.00% 9.13% NA
Japonica Intermediate  241 85.90% 0.00% 0.00% 14.11% NA
VI/Aromatic  96 60.40% 0.00% 1.04% 38.54% NA
Intermediate  90 85.60% 0.00% 0.00% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0712977464 C -> DEL N N silent_mutation Average:9.594; most accessible tissue: Callus, score: 49.721 N N N N
vg0712977464 C -> A LOC_Os07g23010.1 upstream_gene_variant ; 3812.0bp to feature; MODIFIER silent_mutation Average:9.594; most accessible tissue: Callus, score: 49.721 N N N N
vg0712977464 C -> A LOC_Os07g22990-LOC_Os07g23010 intergenic_region ; MODIFIER silent_mutation Average:9.594; most accessible tissue: Callus, score: 49.721 N N N N
vg0712977464 C -> T LOC_Os07g23010.1 upstream_gene_variant ; 3812.0bp to feature; MODIFIER silent_mutation Average:9.594; most accessible tissue: Callus, score: 49.721 N N N N
vg0712977464 C -> T LOC_Os07g22990-LOC_Os07g23010 intergenic_region ; MODIFIER silent_mutation Average:9.594; most accessible tissue: Callus, score: 49.721 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0712977464 7.64E-06 7.43E-06 mr1053 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
vg0712977464 6.08E-06 NA mr1147 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
vg0712977464 5.16E-06 7.19E-06 mr1963 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
vg0712977464 6.29E-06 3.44E-06 mr1963 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