Search for Variation information by Variation ID:
Detailed information for vg1213556772:
| Variant ID: vg1213556772 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13556772 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 108. )
Flanking Sequence (100 bp) in Reference Genome:
CATCCAGGACGAACACGAGGGAAAGGGGTGATTCCTTGGAAGATTGGTTTCAAGGAGGACATCCACACGTACAGGAGTCGGATGAGGAGCAAGAGAGATA[T/C]
CGAGGCAAAGATTGCAGATCTAGAGTTCCGGGTATCGAGCTACGAACTCAACATGCAAGAGGAGGTGGCAAGGAAGGTTGATGAACGCATGGCCGCACAT
Reverse complement sequence
ATGTGCGGCCATGCGTTCATCAACCTTCCTTGCCACCTCCTCTTGCATGTTGAGTTCGTAGCTCGATACCCGGAACTCTAGATCTGCAATCTTTGCCTCG[A/G]
TATCTCTCTTGCTCCTCATCCGACTCCTGTACGTGTGGATGTCCTCCTTGAAACCAATCTTCCAAGGAATCACCCCTTTCCCTCGTGTTCGTCCTGGATG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.30% | 15.80% | 31.53% | 33.31% | NA |
| All Indica | 2759 | 13.60% | 2.00% | 39.94% | 44.44% | NA |
| All Japonica | 1512 | 30.20% | 44.00% | 12.83% | 12.96% | NA |
| Aus | 269 | 18.60% | 1.10% | 47.96% | 32.34% | NA |
| Indica I | 595 | 1.80% | 0.80% | 48.24% | 49.08% | NA |
| Indica II | 465 | 30.10% | 3.70% | 44.52% | 21.72% | NA |
| Indica III | 913 | 12.50% | 0.90% | 36.04% | 50.60% | NA |
| Indica Intermediate | 786 | 14.10% | 3.20% | 35.50% | 47.20% | NA |
| Temperate Japonica | 767 | 8.00% | 78.10% | 8.47% | 5.48% | NA |
| Tropical Japonica | 504 | 65.90% | 1.60% | 17.06% | 15.48% | NA |
| Japonica Intermediate | 241 | 26.10% | 24.50% | 17.84% | 31.54% | NA |
| VI/Aromatic | 96 | 17.70% | 1.00% | 44.79% | 36.46% | NA |
| Intermediate | 90 | 16.70% | 25.60% | 24.44% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1213556772 | T -> C | LOC_Os12g23840.1 | missense_variant ; p.Ile419Thr; MODERATE | nonsynonymous_codon ; I419A | Average:19.655; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 | benign  |
0.608 |
DELETERIOUS | 0.00 |
| vg1213556772 | T -> C | LOC_Os12g23840.1 | missense_variant ; p.Ile419Thr; MODERATE | nonsynonymous_codon ; I419T | Average:19.655; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 | benign |
-0.694 |
TOLERATED | 1.00 |
| vg1213556772 | T -> DEL | LOC_Os12g23840.1 | N | frameshift_variant | Average:19.655; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213556772 | NA | 1.67E-06 | mr1925 | 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 |
| vg1213556772 | NA | 3.93E-10 | mr1050_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 |
| vg1213556772 | NA | 8.66E-06 | mr1050_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 |
| vg1213556772 | NA | 6.64E-06 | mr1158_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 |