| Variant ID: vg1007670489 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670489 |
| Reference Allele: A | Alternative Allele: T,C |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAGATAAGTACAAATGCATCAGTCACAAGGTTATGCCTTCGGTATGATCTGAACGAGCATATGCCACAGGCTCTTGGGGATCATCGTCAAGGTCAATGTG[A/T,C]
GGTCTTACATGAAGATTATGGTTGTATTCTTCTTCATCGACGACGTTGTCAACTCCTACAATTCGGCGCTTTCCATCCCTCACGATGTGCATCTTCTTGT
ACAAGAAGATGCACATCGTGAGGGATGGAAAGCGCCGAATTGTAGGAGTTGACAACGTCGTCGATGAAGAAGAATACAACCATAATCTTCATGTAAGACC[T/A,G]
CACATTGACCTTGACGATGATCCCCAAGAGCCTGTGGCATATGCTCGTTCAGATCATACCGAAGGCATAACCTTGTGACTGATGCATTTGTACTTATCTA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.90% | 0.30% | 2.22% | 17.50% | NA |
| All Indica | 2759 | 81.90% | 0.00% | 2.61% | 15.44% | NA |
| All Japonica | 1512 | 73.20% | 1.10% | 1.72% | 24.01% | NA |
| Aus | 269 | 95.50% | 0.00% | 0.00% | 4.46% | NA |
| Indica I | 595 | 70.80% | 0.00% | 6.89% | 22.35% | NA |
| Indica II | 465 | 78.50% | 0.00% | 2.37% | 19.14% | NA |
| Indica III | 913 | 92.90% | 0.00% | 0.00% | 7.12% | NA |
| Indica Intermediate | 786 | 79.80% | 0.00% | 2.54% | 17.68% | NA |
| Temperate Japonica | 767 | 92.00% | 0.70% | 0.91% | 6.39% | NA |
| Tropical Japonica | 504 | 42.50% | 0.00% | 3.57% | 53.97% | NA |
| Japonica Intermediate | 241 | 77.60% | 4.60% | 0.41% | 17.43% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 3.12% | 13.54% | NA |
| Intermediate | 90 | 81.10% | 0.00% | 4.44% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670489 | A -> C | LOC_Os10g14130.1 | synonymous_variant ; p.Pro474Pro; LOW | N | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |
| vg1007670489 | A -> C | LOC_Os10g14120.1 | upstream_gene_variant ; 2912.0bp to feature; MODIFIER | N | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |
| vg1007670489 | A -> C | LOC_Os10g14140.1 | downstream_gene_variant ; 2523.0bp to feature; MODIFIER | N | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |
| vg1007670489 | A -> C | LOC_Os10g14150.1 | downstream_gene_variant ; 4786.0bp to feature; MODIFIER | N | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |
| vg1007670489 | A -> T | LOC_Os10g14130.1 | synonymous_variant ; p.Pro474Pro; LOW | synonymous_codon | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |
| vg1007670489 | A -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |