Search for Variation information by Variation ID:
Detailed information for vg1213320731:
| Variant ID: vg1213320731 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13320731 |
| Reference Allele: T | Alternative Allele: C,G |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACTTCGTCGCCAAGTGGACCGAGTGCCAAGAAGACACGCCTGCGGAAAAGACAGAGTATTGGACTATGCATTTTGACGGGTCAAAGAGGCTTTCAGGCA[T/C,G]
TGGAGCGGGGGTTGTTCTAATTTCCCCGACTAGAGAGAGGTTGAGCTACGTGTTGTGGATACATTTTTCTGCGTCTCACAACGTGGCGGAATATGAGGCG
Reverse complement sequence
CGCCTCATATTCCGCCACGTTGTGAGACGCAGAAAAATGTATCCACAACACGTAGCTCAACCTCTCTCTAGTCGGGGAAATTAGAACAACCCCCGCTCCA[A/G,C]
TGCCTGAAAGCCTCTTTGACCCGTCAAAATGCATAGTCCAATACTCTGTCTTTTCCGCAGGCGTGTCTTCTTGGCACTCGGTCCACTTGGCGACGAAGTC
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 | 56.80% | 19.80% | 17.94% | 5.12% | G: 0.38% |
| All Indica | 2759 | 70.90% | 6.10% | 19.39% | 2.97% | G: 0.65% |
| All Japonica | 1512 | 22.90% | 48.10% | 18.65% | 10.38% | NA |
| Aus | 269 | 92.60% | 2.60% | 4.09% | 0.74% | NA |
| Indica I | 595 | 54.30% | 11.60% | 30.59% | 3.36% | G: 0.17% |
| Indica II | 465 | 54.40% | 6.50% | 32.26% | 5.38% | G: 1.51% |
| Indica III | 913 | 92.40% | 1.00% | 5.15% | 0.77% | G: 0.66% |
| Indica Intermediate | 786 | 68.30% | 7.50% | 19.85% | 3.82% | G: 0.51% |
| Temperate Japonica | 767 | 3.40% | 82.10% | 6.52% | 7.95% | NA |
| Tropical Japonica | 504 | 50.40% | 6.30% | 30.95% | 12.30% | NA |
| Japonica Intermediate | 241 | 27.40% | 27.00% | 31.54% | 14.11% | NA |
| VI/Aromatic | 96 | 91.70% | 2.10% | 6.25% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 34.40% | 15.56% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213320731 | T -> C | LOC_Os12g23530.1 | missense_variant ; p.Ile293Thr; MODERATE | nonsynonymous_codon ; I293T | Average:17.07; most accessible tissue: Callus, score: 38.748 | benign  |
-0.472 |
TOLERATED | 1.00 |
| vg1213320731 | T -> DEL | LOC_Os12g23530.1 | N | frameshift_variant | Average:17.07; most accessible tissue: Callus, score: 38.748 | N | N | N | N |
| vg1213320731 | T -> G | LOC_Os12g23530.1 | missense_variant ; p.Ile293Ser; MODERATE | nonsynonymous_codon ; I293S | Average:17.07; most accessible tissue: Callus, score: 38.748 | benign |
0.882 |
TOLERATED | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1213320731 | NA | 1.53E-06 | mr1377 | 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 |
| vg1213320731 | 2.10E-06 | 2.10E-06 | mr1377 | 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 |
| vg1213320731 | NA | 9.09E-06 | mr1346_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 |
| vg1213320731 | NA | 3.15E-06 | mr1686_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 |
| vg1213320731 | NA | 5.90E-06 | mr1698_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 |
| vg1213320731 | NA | 3.40E-13 | mr1853_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 |