| Variant ID: vg0121065810 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21065810 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 309. )
AGATGTCAGATTCCCACTGATTCTGACATTGAAAGACTTAGAGAGGAAGAAGATAATGAAGAGGACAATTTCCAAGAGGTGTCTAACAAAAAGAAGAACA[G/T]
GGCTAAGAAAACAGAACTTGCAGTGACTTCAAGGATGAATCTAAGACAAAGGGAGATGGCTGCTAACCCAATAACCAAAAGAACTAAGATACTCACCTAG
CTAGGTGAGTATCTTAGTTCTTTTGGTTATTGGGTTAGCAGCCATCTCCCTTTGTCTTAGATTCATCCTTGAAGTCACTGCAAGTTCTGTTTTCTTAGCC[C/A]
TGTTCTTCTTTTTGTTAGACACCTCTTGGAAATTGTCCTCTTCATTATCTTCTTCCTCTCTAAGTCTTTCAATGTCAGAATCAGTGGGAATCTGACATCT
| 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 | 97.50% | 0.40% | 0.11% | 1.95% | NA |
| All Indica | 2759 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 93.70% | 0.00% | 0.33% | 5.95% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 95.80% | 0.00% | 0.40% | 3.77% | NA |
| Japonica Intermediate | 241 | 70.50% | 0.00% | 1.24% | 28.22% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0121065810 | G -> T | LOC_Os01g37660.1 | missense_variant ; p.Arg117Met; MODERATE | nonsynonymous_codon ; R117M | Average:43.376; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0121065810 | G -> DEL | LOC_Os01g37660.1 | N | frameshift_variant | Average:43.376; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 | N | N | N | N |