| Variant ID: vg0904847668 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4847668 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 281. )
TGGAGTTAGGCTGAAACTGGAATCTTGGCGAGGATTTGTGTTTCCTTGATGCTTCCCTCCGTTGGAACTGGCGGGTTGGTTGGCCATCTTCTTCGTCAGC[A/G]
GAAAACTGAATCGACAATCTTTTGGTACATGATCAGTTCCTTCACAAAAGAAACAAGTGATCCTGCTCGTTGGACACCTATCGGGTGGATGGTCTTCCTC
GAGGAAGACCATCCACCCGATAGGTGTCCAACGAGCAGGATCACTTGTTTCTTTTGTGAAGGAACTGATCATGTACCAAAAGATTGTCGATTCAGTTTTC[T/C]
GCTGACGAAGAAGATGGCCAACCAACCCGCCAGTTCCAACGGAGGGAAGCATCAAGGAAACACAAATCCTCGCCAAGATTCCAGTTTCAGCCTAACTCCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.60% | 0.60% | 4.72% | 75.10% | NA |
| All Indica | 2759 | 7.20% | 0.00% | 2.75% | 90.07% | NA |
| All Japonica | 1512 | 37.60% | 1.70% | 8.40% | 52.31% | NA |
| Aus | 269 | 21.60% | 0.00% | 2.60% | 75.84% | NA |
| Indica I | 595 | 6.90% | 0.00% | 1.68% | 91.43% | NA |
| Indica II | 465 | 7.70% | 0.00% | 2.15% | 90.11% | NA |
| Indica III | 913 | 4.60% | 0.00% | 3.83% | 91.57% | NA |
| Indica Intermediate | 786 | 10.10% | 0.00% | 2.67% | 87.28% | NA |
| Temperate Japonica | 767 | 45.40% | 0.00% | 4.43% | 50.20% | NA |
| Tropical Japonica | 504 | 25.20% | 1.40% | 8.73% | 64.68% | NA |
| Japonica Intermediate | 241 | 39.00% | 7.50% | 20.33% | 33.20% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 7.29% | 13.54% | NA |
| Intermediate | 90 | 27.80% | 3.30% | 6.67% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904847668 | A -> G | LOC_Os09g09070.1 | missense_variant ; p.Leu257Pro; MODERATE | nonsynonymous_codon ; L257P | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0904847668 | A -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |