| Variant ID: vg0420967319 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20967319 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGCGTCCCCGCATCCACCATGGACCGCTTCCACAAGATCGTCCTCAGCTGGGACTACTTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCC[C/T]
GCCCCGAGCGCTCGCTTTGCAATCACCGGCACCACCTTTGAATTTTTTTTCTATATGGCGGCTTGGGAGGACAGGGCGGGCAGCAGCAGGCGAAGGGGCT
AGCCCCTTCGCCTGCTGCTGCCCGCCCTGTCCTCCCAAGCCGCCATATAGAAAAAAAATTCAAAGGTGGTGCCGGTGATTGCAAAGCGAGCGCTCGGGGC[G/A]
GGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGAAGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGATGCGGGGACGCCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.10% | 7.10% | 21.98% | 13.86% | NA |
| All Indica | 2759 | 40.10% | 12.10% | 29.10% | 18.77% | NA |
| All Japonica | 1512 | 91.70% | 0.00% | 1.85% | 6.42% | NA |
| Aus | 269 | 32.30% | 0.00% | 65.80% | 1.86% | NA |
| Indica I | 595 | 77.30% | 4.50% | 11.26% | 6.89% | NA |
| Indica II | 465 | 15.50% | 14.40% | 33.76% | 36.34% | NA |
| Indica III | 913 | 36.00% | 16.90% | 32.09% | 15.01% | NA |
| Indica Intermediate | 786 | 31.00% | 10.80% | 36.39% | 21.76% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 79.00% | 0.00% | 4.56% | 16.47% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 1.66% | 5.81% | NA |
| VI/Aromatic | 96 | 56.20% | 0.00% | 16.67% | 27.08% | NA |
| Intermediate | 90 | 71.10% | 2.20% | 16.67% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967319 | C -> DEL | N | N | silent_mutation | Average:36.43; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0420967319 | C -> T | LOC_Os04g34650.1 | upstream_gene_variant ; 2651.0bp to feature; MODIFIER | silent_mutation | Average:36.43; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg0420967319 | C -> T | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.43; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |