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Detailed information for vg0615112996:

Variant ID: vg0615112996 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15112996
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCGCTTTGATTTTATACTTTTTGGGGGGTCTCCAAGCATCCATCTTCCACACCTTGGACTAATGCACCTGAAAGCTACTCAATGAGCTCATTAGTCCCT[T/C]
AACCACATTTGTCATTAATCACCAAAACCCACTAGGAGGATTAATGCACTTTCAAACTCCCTGTACTCCTTGGGAGTTGTCACCTTGATTTCCTTGAGAA

Reverse complement sequence

TTCTCAAGGAAATCAAGGTGACAACTCCCAAGGAGTACAGGGAGTTTGAAAGTGCATTAATCCTCCTAGTGGGTTTTGGTGATTAATGACAAATGTGGTT[A/G]
AGGGACTAATGAGCTCATTGAGTAGCTTTCAGGTGCATTAGTCCAAGGTGTGGAAGATGGATGCTTGGAGACCCCCCAAAAAGTATAAAATCAAAGCGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.30% 29.20% 0.61% 32.90% NA
All Indica  2759 4.50% 44.10% 0.62% 50.82% NA
All Japonica  1512 91.30% 6.10% 0.60% 2.05% NA
Aus  269 70.30% 17.10% 0.37% 12.27% NA
Indica I  595 8.20% 12.90% 0.50% 78.32% NA
Indica II  465 2.60% 23.90% 1.08% 72.47% NA
Indica III  913 1.00% 79.20% 0.77% 19.06% NA
Indica Intermediate  786 6.70% 38.90% 0.25% 54.07% NA
Temperate Japonica  767 96.70% 2.00% 0.00% 1.30% NA
Tropical Japonica  504 82.30% 12.90% 1.79% 2.98% NA
Japonica Intermediate  241 92.50% 5.00% 0.00% 2.49% NA
VI/Aromatic  96 26.00% 4.20% 1.04% 68.75% NA
Intermediate  90 51.10% 22.20% 1.11% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0615112996 T -> C LOC_Os06g25860.1 downstream_gene_variant ; 1530.0bp to feature; MODIFIER silent_mutation Average:8.896; most accessible tissue: Callus, score: 18.91 N N N N
vg0615112996 T -> C LOC_Os06g25860-LOC_Os06g25870 intergenic_region ; MODIFIER silent_mutation Average:8.896; most accessible tissue: Callus, score: 18.91 N N N N
vg0615112996 T -> DEL N N silent_mutation Average:8.896; most accessible tissue: Callus, score: 18.91 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615112996 NA 7.18E-06 mr1011 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
vg0615112996 NA 2.62E-07 mr1020 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
vg0615112996 1.52E-07 1.52E-07 mr1032 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
vg0615112996 NA 4.04E-08 mr1162 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
vg0615112996 3.61E-06 3.61E-06 mr1165 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
vg0615112996 1.68E-08 1.68E-08 mr1478 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
vg0615112996 1.43E-07 1.43E-07 mr1536 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
vg0615112996 4.88E-06 4.88E-06 mr1828 Ind_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
vg0615112996 5.34E-06 7.28E-09 mr1971 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
vg0615112996 6.50E-06 5.48E-09 mr1165_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
vg0615112996 6.57E-06 4.18E-09 mr1536_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
vg0615112996 8.88E-06 8.88E-06 mr1971_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