| Variant ID: vg0114587626 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587626 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )
TGAAGAATTCAGCAGAAGAAAGATTATGTTCTTGGTTTTCCATAGTCCACATCATGGTCCACATTTGGAGGGAAAATGAAAATTGAGACAGTACCGAGTA[G/T]
ATATCTCCATATATTTGTACCTCTGAAGAGAACAATCCCTGATACAAATTACTGATGCAAAAATAAGTTGTTTTCGGCCCCCATAGACATTATGAAATTC
GAATTTCATAATGTCTATGGGGGCCGAAAACAACTTATTTTTGCATCAGTAATTTGTATCAGGGATTGTTCTCTTCAGAGGTACAAATATATGGAGATAT[C/A]
TACTCGGTACTGTCTCAATTTTCATTTTCCCTCCAAATGTGGACCATGATGTGGACTATGGAAAACCAAGAACATAATCTTTCTTCTGCTGAATTCTTCA
| 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 | 79.40% | 0.10% | 1.48% | 18.96% | NA |
| All Indica | 2759 | 65.30% | 0.30% | 2.43% | 32.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 50.80% | 0.00% | 1.01% | 48.24% | NA |
| Indica II | 465 | 71.00% | 0.00% | 0.65% | 28.39% | NA |
| Indica III | 913 | 70.30% | 0.30% | 2.63% | 26.73% | NA |
| Indica Intermediate | 786 | 67.20% | 0.50% | 4.33% | 27.99% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 0.00% | 3.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587626 | G -> T | LOC_Os01g25740.1 | missense_variant ; p.Leu1343Ile; MODERATE | nonsynonymous_codon ; L1343I | Average:63.133; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | unknown | unknown | TOLERATED | 0.35 |
| vg0114587626 | G -> DEL | LOC_Os01g25740.1 | N | frameshift_variant | Average:63.133; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |