| Variant ID: vg1204378238 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4378238 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAGCTCCCGCGTCCGCTCTCTCCTTCGCTCCAGCATTAGCCGCCAGGGGTCCAGCCAGTGGCAACGGGGGTTGGTTGCCTGCTACTCCCAGTGGCAGCCG[C/T]
GACCACAGCAGCAGCAGTTCCAGTGGCTCGGAGCCGGGCAGCGGCGAGATGTATCTGCCAAACTCCAGGAGCCGCTCAGAGGGACGTGGTGACGAGCAGG
CCTGCTCGTCACCACGTCCCTCTGAGCGGCTCCTGGAGTTTGGCAGATACATCTCGCCGCTGCCCGGCTCCGAGCCACTGGAACTGCTGCTGCTGTGGTC[G/A]
CGGCTGCCACTGGGAGTAGCAGGCAACCAACCCCCGTTGCCACTGGCTGGACCCCTGGCGGCTAATGCTGGAGCGAAGGAGAGAGCGGACGCGGGAGCTG
| 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 | 80.00% | 4.60% | 8.36% | 7.00% | NA |
| All Indica | 2759 | 80.90% | 5.90% | 10.66% | 2.50% | NA |
| All Japonica | 1512 | 79.20% | 0.70% | 3.64% | 16.53% | NA |
| Aus | 269 | 69.10% | 15.20% | 14.13% | 1.49% | NA |
| Indica I | 595 | 78.20% | 11.60% | 9.75% | 0.50% | NA |
| Indica II | 465 | 84.90% | 2.80% | 9.25% | 3.01% | NA |
| Indica III | 913 | 79.30% | 4.80% | 11.94% | 3.94% | NA |
| Indica Intermediate | 786 | 82.40% | 4.80% | 10.69% | 2.04% | NA |
| Temperate Japonica | 767 | 88.80% | 0.00% | 1.43% | 9.78% | NA |
| Tropical Japonica | 504 | 76.00% | 2.00% | 6.35% | 15.67% | NA |
| Japonica Intermediate | 241 | 55.20% | 0.00% | 4.98% | 39.83% | NA |
| VI/Aromatic | 96 | 87.50% | 1.00% | 6.25% | 5.21% | NA |
| Intermediate | 90 | 93.30% | 1.10% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204378238 | C -> DEL | LOC_Os12g08610.1 | N | frameshift_variant | Average:12.199; most accessible tissue: Callus, score: 35.2 | N | N | N | N |
| vg1204378238 | C -> T | LOC_Os12g08610.1 | stop_gained ; p.Arg326*; HIGH | stop_gained | Average:12.199; most accessible tissue: Callus, score: 35.2 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204378238 | NA | 6.49E-07 | mr1308 | 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 |
| vg1204378238 | 3.78E-06 | 3.78E-06 | mr1753_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 |