| Variant ID: vg1220235213 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20235213 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCTTGACCTTGTTGGTGATCGGGAGAGACAAGCCTACTATATGCTAGCCGACCGGGAGTATGCTCACACGCGAGAATACTCACCGGAGCTGATAAAAAA[G/T]
ATAGGTATGGATACTGAATTTCGTGCTATTTGGAAAGCTGTTGGTTGGCAGAAATTTGCTATGGTAGATGAGCCTGGTTCTCGTTTGCTTACTTTGCAAT
ATTGCAAAGTAAGCAAACGAGAACCAGGCTCATCTACCATAGCAAATTTCTGCCAACCAACAGCTTTCCAAATAGCACGAAATTCAGTATCCATACCTAT[C/A]
TTTTTTATCAGCTCCGGTGAGTATTCTCGCGTGTGAGCATACTCCCGGTCGGCTAGCATATAGTAGGCTTGTCTCTCCCGATCACCAACAAGGTCAAGAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.60% | 1.80% | 2.67% | 22.87% | NA |
| All Indica | 2759 | 71.80% | 2.10% | 2.39% | 23.67% | NA |
| All Japonica | 1512 | 83.20% | 0.70% | 1.12% | 15.01% | NA |
| Aus | 269 | 36.40% | 5.90% | 14.13% | 43.49% | NA |
| Indica I | 595 | 77.60% | 2.20% | 2.02% | 18.15% | NA |
| Indica II | 465 | 72.30% | 0.20% | 1.51% | 26.02% | NA |
| Indica III | 913 | 68.20% | 2.70% | 2.96% | 26.07% | NA |
| Indica Intermediate | 786 | 71.20% | 2.50% | 2.54% | 23.66% | NA |
| Temperate Japonica | 767 | 96.10% | 0.00% | 0.13% | 3.78% | NA |
| Tropical Japonica | 504 | 67.10% | 1.40% | 2.78% | 28.77% | NA |
| Japonica Intermediate | 241 | 75.90% | 1.20% | 0.83% | 21.99% | NA |
| VI/Aromatic | 96 | 29.20% | 0.00% | 3.12% | 67.71% | NA |
| Intermediate | 90 | 74.40% | 2.20% | 2.22% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220235213 | G -> DEL | LOC_Os12g33500.1 | N | frameshift_variant | Average:11.334; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1220235213 | G -> T | LOC_Os12g33500.1 | missense_variant ; p.Lys79Asn; MODERATE | nonsynonymous_codon ; K79N | Average:11.334; most accessible tissue: Minghui63 panicle, score: 25.313 | unknown | unknown | TOLERATED | 0.06 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1220235213 | 3.61E-06 | 3.61E-06 | mr1421 | 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 |
| vg1220235213 | 4.77E-06 | NA | mr1457 | 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 |
| vg1220235213 | 7.80E-06 | NA | mr1912 | 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 |