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Detailed information for vg1220340557:

Variant ID: vg1220340557 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20340557
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


GCAGAGGAGAAAGTCAGAACCGTCAGAGAAAGGCTAAGAATTGCGCAATCTCGACAGAAGAGTTATGCTGACAACCGCCAAAGAGAGCTTACTTTCGAAG[T/C]
AGGGGATTATGTGTACCTTCGTGTCACTCCGCTCAGGGGAGTACACCGCTTCCAGACTAAAGGAAAGTTGGCACCACGCTTTGTGGGACCATACAGGATC

Reverse complement sequence

GATCCTGTATGGTCCCACAAAGCGTGGTGCCAACTTTCCTTTAGTCTGGAAGCGGTGTACTCCCCTGAGCGGAGTGACACGAAGGTACACATAATCCCCT[A/G]
CTTCGAAAGTAAGCTCTCTTTGGCGGTTGTCAGCATAACTCTTCTGTCGAGATTGCGCAATTCTTAGCCTTTCTCTGACGGTTCTGACTTTCTCCTCTGC

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 46.20% 33.70% 7.32% 12.76% NA
All Indica  2759 70.00% 17.10% 10.91% 2.03% NA
All Japonica  1512 1.70% 68.50% 1.32% 28.44% NA
Aus  269 68.00% 13.80% 5.58% 12.64% NA
Indica I  595 46.60% 38.70% 11.09% 3.70% NA
Indica II  465 65.40% 17.80% 16.34% 0.43% NA
Indica III  913 88.00% 3.50% 6.46% 2.08% NA
Indica Intermediate  786 69.50% 16.20% 12.72% 1.65% NA
Temperate Japonica  767 0.30% 94.70% 0.39% 4.69% NA
Tropical Japonica  504 4.80% 30.00% 2.78% 62.50% NA
Japonica Intermediate  241 0.00% 66.00% 1.24% 32.78% NA
VI/Aromatic  96 7.30% 11.50% 3.12% 78.12% NA
Intermediate  90 41.10% 42.20% 7.78% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220340557 T -> C LOC_Os12g33690.1 missense_variant ; p.Val1162Ala; MODERATE nonsynonymous_codon ; V1162A Average:15.146; most accessible tissue: Callus, score: 39.213 unknown unknown TOLERATED 1.00
vg1220340557 T -> DEL LOC_Os12g33690.1 N frameshift_variant Average:15.146; most accessible tissue: Callus, score: 39.213 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220340557 2.89E-14 2.83E-93 mr1334 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
vg1220340557 1.80E-07 1.50E-11 mr1334 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
vg1220340557 6.34E-06 NA mr1334 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
vg1220340557 NA 7.84E-21 mr1698 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
vg1220340557 NA 1.32E-06 mr1750 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
vg1220340557 1.73E-15 6.10E-103 mr1334_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
vg1220340557 4.30E-15 8.69E-20 mr1334_2 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
vg1220340557 2.88E-08 7.82E-55 mr1991_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
vg1220340557 7.76E-06 7.76E-06 mr1991_2 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
vg1220340557 NA 1.74E-08 mr1991_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