| Variant ID: vg0420967349 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 20967349 |
| Reference Allele: C | Alternative Allele: CACCATGG,T |
| Primary Allele: C | Secondary Allele: CACCATGG |
Inferred Ancestral Allele: Not determined.
CCACAAGATCGTCCTCAGCTGGGACTACTTCCGCCTCGTCGCGGACTCCAAGGTACGCCCCTCCCCGCCCCGCCCCGAGCGCTCGCTTTGCAATCACCGG[C/CACCATGG,T]
ACCACCTTTGAATTTTTTTTCTATATGGCGGCTTGGGAGGACAGGGCGGGCAGCAGCAGGCGAAGGGGCTGGGGCGCGTGAAGAACACGTACGCCTCGGT
ACCGAGGCGTACGTGTTCTTCACGCGCCCCAGCCCCTTCGCCTGCTGCTGCCCGCCCTGTCCTCCCAAGCCGCCATATAGAAAAAAAATTCAAAGGTGGT[G/CCATGGTG,A]
CCGGTGATTGCAAAGCGAGCGCTCGGGGCGGGGCGGGGAGGGGCGTACCTTGGAGTCCGCGACGAGGCGGAAGTAGTCCCAGCTGAGGACGATCTTGTGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CACCATGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.40% | 0.50% | 7.81% | 3.26% | T: 0.04% |
| All Indica | 2759 | 93.30% | 0.40% | 5.69% | 0.51% | T: 0.07% |
| All Japonica | 1512 | 91.90% | 0.10% | 1.06% | 6.94% | NA |
| Aus | 269 | 27.10% | 4.80% | 66.91% | 1.12% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.60% | 0.00% | 3.23% | 0.22% | NA |
| Indica III | 913 | 89.40% | 0.90% | 9.09% | 0.44% | T: 0.22% |
| Indica Intermediate | 786 | 91.00% | 0.40% | 7.51% | 1.15% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 79.20% | 0.20% | 2.78% | 17.86% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.83% | 6.22% | NA |
| VI/Aromatic | 96 | 61.50% | 0.00% | 10.42% | 28.12% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 6.67% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420967349 | C -> DEL | N | N | silent_mutation | Average:41.666; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0420967349 | C -> CACCATGG | LOC_Os04g34650.1 | upstream_gene_variant ; 2682.0bp to feature; MODIFIER | silent_mutation | Average:41.666; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0420967349 | C -> CACCATGG | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.666; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0420967349 | C -> T | LOC_Os04g34650.1 | upstream_gene_variant ; 2681.0bp to feature; MODIFIER | silent_mutation | Average:41.666; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |
| vg0420967349 | C -> T | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.666; most accessible tissue: Zhenshan97 panicle, score: 72.468 | N | N | N | N |