| Variant ID: vg0202540151 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2540151 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 304. )
GATACGCGGCGTACCAAAAGACGTCAGATCATATGATGTCAAACAAGTACGCGGTAAGAGTAATTGGTAGATTGGTTTTTTAAATTAATCTACTAATTTC[G/A]
TAGATACATCCGGCATGTATCTACAAAGGTACGCAATATTTTATATGCAATTTATCATACCTATTCAGATCATACAGAATTGTCAGATCTATAATTTATT
AATAAATTATAGATCTGACAATTCTGTATGATCTGAATAGGTATGATAAATTGCATATAAAATATTGCGTACCTTTGTAGATACATGCCGGATGTATCTA[C/T]
GAAATTAGTAGATTAATTTAAAAAACCAATCTACCAATTACTCTTACCGCGTACTTGTTTGACATCATATGATCTGACGTCTTTTGGTACGCCGCGTATC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.70% | 0.80% | 0.49% | 0.00% | NA |
| All Indica | 2759 | 97.90% | 1.30% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 0.30% | 1.85% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.60% | 3.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 0.50% | 1.27% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202540151 | G -> A | LOC_Os02g05270.1 | upstream_gene_variant ; 3976.0bp to feature; MODIFIER | silent_mutation | Average:41.111; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540151 | G -> A | LOC_Os02g05280.1 | downstream_gene_variant ; 1481.0bp to feature; MODIFIER | silent_mutation | Average:41.111; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540151 | G -> A | LOC_Os02g05300.1 | downstream_gene_variant ; 1939.0bp to feature; MODIFIER | silent_mutation | Average:41.111; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540151 | G -> A | LOC_Os02g05290.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.111; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |