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Detailed information for vg1213276842:

Variant ID: vg1213276842 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13276842
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, C: 0.29, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTCCGATTGCTTTGGTGTTTGACCAAATCTCTTCCTACGAGATGATCTTGGTCTTTTCGAATCACTAGTTTGATTATCAAATCGTTGACCAGCTAATC[C/A]
TTTTTTGTACTTAGCCATAAACATCTCAAAAGTGAGCTTCGGCTTTTTGGTCTTGTTGGAACTAGATGACTCATCTTTTGTAACCTTACGATCTTCAGCC

Reverse complement sequence

GGCTGAAGATCGTAAGGTTACAAAAGATGAGTCATCTAGTTCCAACAAGACCAAAAAGCCGAAGCTCACTTTTGAGATGTTTATGGCTAAGTACAAAAAA[G/T]
GATTAGCTGGTCAACGATTTGATAATCAAACTAGTGATTCGAAAAGACCAAGATCATCTCGTAGGAAGAGATTTGGTCAAACACCAAAGCAATCGGAGCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.20% 18.40% 4.53% 40.90% NA
All Indica  2759 41.80% 4.40% 3.66% 50.20% NA
All Japonica  1512 15.80% 47.50% 6.02% 30.69% NA
Aus  269 79.90% 1.10% 2.97% 15.99% NA
Indica I  595 15.80% 6.70% 4.20% 73.28% NA
Indica II  465 54.40% 5.20% 3.87% 36.56% NA
Indica III  913 43.60% 3.20% 4.27% 48.96% NA
Indica Intermediate  786 51.80% 3.60% 2.42% 42.24% NA
Temperate Japonica  767 9.30% 78.10% 1.30% 11.34% NA
Tropical Japonica  504 16.30% 10.90% 12.90% 59.92% NA
Japonica Intermediate  241 35.70% 26.60% 6.64% 31.12% NA
VI/Aromatic  96 70.80% 1.00% 10.42% 17.71% NA
Intermediate  90 41.10% 27.80% 4.44% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1213276842 C -> DEL LOC_Os12g23480.1 N frameshift_variant Average:8.126; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg1213276842 C -> A LOC_Os12g23480.1 stop_gained ; p.Gly122*; HIGH stop_gained Average:8.126; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213276842 NA 1.97E-06 mr1156 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
vg1213276842 NA 2.26E-07 mr1803 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
vg1213276842 NA 2.86E-07 mr1346_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
vg1213276842 NA 2.41E-08 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
vg1213276842 NA 1.35E-06 mr1577_2 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
vg1213276842 NA 4.26E-06 mr1629_2 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
vg1213276842 NA 3.95E-06 mr1780_2 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
vg1213276842 NA 1.29E-10 mr1792_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
vg1213276842 NA 5.56E-07 mr1792_2 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
vg1213276842 NA 3.53E-13 mr1803_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
vg1213276842 NA 1.74E-07 mr1803_2 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