| Variant ID: vg1000678017 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 678017 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 300. )
ATATGTTCCCTGAAACATGGGCTGCCACTGTACAGTTTCAGGAAGTACTACAGTGTAGGAAGAGGTTATCTTAGCATATAAACCAGATTCTGAACCATTC[G/C]
TGCACCATGAGATGGATTGATCACTAGTGTGCTACCTGATAGGACGACAACATCGGTTGTGTCGAGGCCGACATCATTGAACTTCTGTATGATCGATTTG
CAAATCGATCATACAGAAGTTCAATGATGTCGGCCTCGACACAACCGATGTTGTCGTCCTATCAGGTAGCACACTAGTGATCAATCCATCTCATGGTGCA[C/G]
GAATGGTTCAGAATCTGGTTTATATGCTAAGATAACCTCTTCCTACACTGTAGTACTTCCTGAAACTGTACAGTGGCAGCCCATGTTTCAGGGAACATAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 89.70% | 10.20% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 82.60% | 17.20% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 83.20% | 16.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 79.50% | 20.40% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 77.70% | 21.90% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000678017 | G -> C | LOC_Os10g02080.1 | downstream_gene_variant ; 2082.0bp to feature; MODIFIER | silent_mutation | Average:76.301; most accessible tissue: Zhenshan97 young leaf, score: 84.814 | N | N | N | N |
| vg1000678017 | G -> C | LOC_Os10g02070.1 | intron_variant ; MODIFIER | silent_mutation | Average:76.301; most accessible tissue: Zhenshan97 young leaf, score: 84.814 | N | N | N | N |