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Detailed information for vg1219872223:

Variant ID: vg1219872223 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19872223
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGTGCCTCCTGAATTCATTGAAAAGCCTGTCGAGAACGAAGAACGGTATTTGGTTATCGACCAGGAGGAGGTCGTAGTATATGCTGTTCGACATCAAC[T/C]
GCATGTGATTGTCGACATGGGCATGGTCTCCCTCTCTCCACTGGAGGAGGAGCTCGACGATGAAGCACCCGTCACGCGTGAGCATGTCCGCGGTGTACAA

Reverse complement sequence

TTGTACACCGCGGACATGCTCACGCGTGACGGGTGCTTCATCGTCGAGCTCCTCCTCCAGTGGAGAGAGGGAGACCATGCCCATGTCGACAATCACATGC[A/G]
GTTGATGTCGAACAGCATATACTACGACCTCCTCCTGGTCGATAACCAAATACCGTTCTTCGTTCTCGACAGGCTTTTCAATGAATTCAGGAGGCACATG

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 68.60% 8.20% 4.04% 19.15% NA
All Indica  2759 67.40% 0.30% 1.16% 31.10% NA
All Japonica  1512 64.40% 24.30% 9.59% 1.72% NA
Aus  269 95.20% 0.00% 1.12% 3.72% NA
Indica I  595 74.10% 0.20% 2.02% 23.70% NA
Indica II  465 62.40% 1.10% 0.65% 35.91% NA
Indica III  913 67.00% 0.00% 0.00% 32.97% NA
Indica Intermediate  786 65.80% 0.40% 2.16% 31.68% NA
Temperate Japonica  767 40.70% 45.80% 13.17% 0.39% NA
Tropical Japonica  504 90.90% 0.40% 4.76% 3.97% NA
Japonica Intermediate  241 84.60% 5.80% 8.30% 1.24% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 64.40% 12.20% 12.22% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1219872223 T -> C LOC_Os12g32880.1 missense_variant ; p.Gln115Arg; MODERATE nonsynonymous_codon ; Q115R Average:51.739; most accessible tissue: Callus, score: 79.057 unknown unknown TOLERATED 1.00
vg1219872223 T -> DEL LOC_Os12g32880.1 N frameshift_variant Average:51.739; most accessible tissue: Callus, score: 79.057 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219872223 NA 1.07E-06 mr1163 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
vg1219872223 NA 6.96E-10 mr1486 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
vg1219872223 NA 6.38E-23 mr1010_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
vg1219872223 NA 4.94E-13 mr1010_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
vg1219872223 NA 8.40E-10 mr1011_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
vg1219872223 NA 4.13E-07 mr1011_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
vg1219872223 NA 6.98E-07 mr1013_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
vg1219872223 NA 1.12E-07 mr1137_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
vg1219872223 1.07E-08 NA mr1486_2 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
vg1219872223 9.50E-07 4.62E-15 mr1486_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
vg1219872223 NA 3.01E-06 mr1588_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
vg1219872223 NA 1.45E-06 mr1617_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