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Detailed information for vg0618222588:

Variant ID: vg0618222588 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 18222588
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAGCTTCGCAGATCCCTCGTCGATGGCGGCAGTGCACTCAACATCCTCTTCGCCAATACCTTGGACGACATGCAGATCCCTCGCACAGAATTAAAACCG[A/T]
GTAATGCGCCCTTTCACGGAGTCATTCCAGGGCTATCCGCTACGCCACTCGGCCAGATCACTCTTCCGGTTACTTTTGGTACTCGGGAGAACTTCCGCAC

Reverse complement sequence

GTGCGGAAGTTCTCCCGAGTACCAAAAGTAACCGGAAGAGTGATCTGGCCGAGTGGCGTAGCGGATAGCCCTGGAATGACTCCGTGAAAGGGCGCATTAC[T/A]
CGGTTTTAATTCTGTGCGAGGGATCTGCATGTCGTCCAAGGTATTGGCGAAGAGGATGTTGAGTGCACTGCCGCCATCGACGAGGGATCTGCGAAGCTTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.40% 4.30% 10.33% 27.02% NA
All Indica  2759 44.40% 0.40% 14.86% 40.34% NA
All Japonica  1512 80.40% 12.60% 2.91% 4.10% NA
Aus  269 58.40% 0.00% 10.04% 31.60% NA
Indica I  595 46.90% 1.70% 12.10% 39.33% NA
Indica II  465 45.20% 0.00% 14.19% 40.65% NA
Indica III  913 40.90% 0.00% 18.18% 40.96% NA
Indica Intermediate  786 46.10% 0.30% 13.49% 40.20% NA
Temperate Japonica  767 73.40% 20.60% 4.43% 1.56% NA
Tropical Japonica  504 89.10% 0.00% 1.79% 9.13% NA
Japonica Intermediate  241 84.60% 13.30% 0.41% 1.66% NA
VI/Aromatic  96 96.90% 1.00% 2.08% 0.00% NA
Intermediate  90 75.60% 0.00% 5.56% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0618222588 A -> T LOC_Os06g31310.1 missense_variant ; p.Ser708Cys; MODERATE nonsynonymous_codon ; S708C Average:11.305; most accessible tissue: Callus, score: 22.485 probably damaging 3.151 DELETERIOUS 0.00
vg0618222588 A -> DEL LOC_Os06g31310.1 N frameshift_variant Average:11.305; most accessible tissue: Callus, score: 22.485 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0618222588 NA 1.06E-06 mr1884 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
vg0618222588 NA 9.89E-07 mr1062_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
vg0618222588 NA 4.67E-06 mr1091_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
vg0618222588 NA 5.43E-06 mr1126_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
vg0618222588 NA 5.17E-06 mr1346_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
vg0618222588 2.64E-06 1.53E-07 mr1456_2 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
vg0618222588 4.55E-06 2.70E-09 mr1456_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
vg0618222588 NA 3.94E-06 mr1565_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
vg0618222588 NA 7.47E-06 mr1577_2 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
vg0618222588 NA 4.23E-06 mr1693_2 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
vg0618222588 NA 4.17E-06 mr1726_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
vg0618222588 NA 5.16E-07 mr1780_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