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Detailed information for vg1220063865:

Variant ID: vg1220063865 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20063865
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGAAAACGATCCTAAGAGTCCTTAGCTCTGTCAAATTACCAATCTCTTTTATTACCTTTCGGGTAGCTTCTATTACAAGCTCCTGTAAAGATTTCATAT[T/C]
CCCCAGCATCAGACCTTGCGCCAGCTTCACTCTGCCAGCATATAGCCGCAACAGTTTCCTTAGTTTGGCAAAAGACATTGGAAACAGTACCTTATGAGAT

Reverse complement sequence

ATCTCATAAGGTACTGTTTCCAATGTCTTTTGCCAAACTAAGGAAACTGTTGCGGCTATATGCTGGCAGAGTGAAGCTGGCGCAAGGTCTGATGCTGGGG[A/G]
ATATGAAATCTTTACAGGAGCTTGTAATAGAAGCTACCCGAAAGGTAATAAAAGAGATTGGTAATTTGACAGAGCTAAGGACTCTTAGGATCGTTTTCGG

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 43.60% 22.00% 7.00% 27.36% NA
All Indica  2759 68.00% 2.00% 11.42% 18.52% NA
All Japonica  1512 2.40% 60.00% 0.13% 37.43% NA
Aus  269 40.90% 16.00% 2.97% 40.15% NA
Indica I  595 56.50% 3.70% 9.08% 30.76% NA
Indica II  465 73.80% 3.70% 17.42% 5.16% NA
Indica III  913 68.30% 0.90% 9.09% 21.69% NA
Indica Intermediate  786 73.00% 1.10% 12.34% 13.49% NA
Temperate Japonica  767 1.70% 88.40% 0.13% 9.78% NA
Tropical Japonica  504 3.20% 22.20% 0.20% 74.40% NA
Japonica Intermediate  241 3.30% 48.50% 0.00% 48.13% NA
VI/Aromatic  96 13.50% 4.20% 1.04% 81.25% NA
Intermediate  90 27.80% 33.30% 5.56% 33.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220063865 T -> C LOC_Os12g33160.1 missense_variant ; p.Asn686Asp; MODERATE nonsynonymous_codon Average:53.755; most accessible tissue: Minghui63 young leaf, score: 74.007 unknown unknown TOLERATED 0.31
vg1220063865 T -> DEL LOC_Os12g33160.1 N frameshift_variant Average:53.755; most accessible tissue: Minghui63 young leaf, score: 74.007 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220063865 NA 2.16E-06 mr1126 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
vg1220063865 1.20E-13 7.06E-90 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
vg1220063865 NA 3.14E-06 mr1538 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
vg1220063865 2.35E-13 8.20E-97 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
vg1220063865 NA 1.85E-10 mr1667_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
vg1220063865 8.90E-06 1.07E-51 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