| Variant ID: vg0221477121 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 21477121 |
| Reference Allele: T | Alternative Allele: TTCC,C |
| Primary Allele: TTCC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGACGCACCGGGAGCATTGACGTTGGGCGGCGGAGCGGCCTGGTTCGCCGGCGGGCCGTAGCTGTCCTCCTCGGCGCCTCCGCAGCAAGACATCTTCTTC[T/TTCC,C]
TCCTCCTCCTCCTCTCGCCGGAGTTGGATGCGCGGGCTGATCTGGTGGCCGCCCCCCGCTCAGCGGATCATCGCGCACGACCTGCAAACCATTTTCGATT
AATCGAAAATGGTTTGCAGGTCGTGCGCGATGATCCGCTGAGCGGGGGGCGGCCACCAGATCAGCCCGCGCATCCAACTCCGGCGAGAGGAGGAGGAGGA[A/GGAA,G]
GAAGAAGATGTCTTGCTGCGGAGGCGCCGAGGAGGACAGCTACGGCCCGCCGGCGAACCAGGCCGCTCCGCCGCCCAACGTCAATGCTCCCGGTGCGTCT
| Populations | Population Size | Frequency of TTCC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.50% | 35.40% | 0.13% | 0.00% | C: 0.02% |
| All Indica | 2759 | 97.00% | 2.80% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 3.60% | 96.30% | 0.00% | 0.00% | C: 0.07% |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.00% | 2.50% | 0.50% | 0.00% | NA |
| Indica II | 465 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 1.90% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 96.90% | 2.90% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 1.30% | 98.60% | 0.00% | 0.00% | C: 0.13% |
| Tropical Japonica | 504 | 6.70% | 93.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.60% | 95.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 46.70% | 52.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221477121 | T -> TTCC | LOC_Os02g35760.1 | 5_prime_UTR_variant ; 9.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> TTCC | LOC_Os02g35760.2 | 5_prime_UTR_variant ; 9.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> TTCC | LOC_Os02g35750.1 | downstream_gene_variant ; 3300.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> TTCC | LOC_Os02g35750.2 | downstream_gene_variant ; 1654.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> TTCC | LOC_Os02g35750.3 | downstream_gene_variant ; 1489.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> C | LOC_Os02g35760.1 | 5_prime_UTR_variant ; 8.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> C | LOC_Os02g35760.2 | 5_prime_UTR_variant ; 8.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> C | LOC_Os02g35750.1 | downstream_gene_variant ; 3299.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> C | LOC_Os02g35750.2 | downstream_gene_variant ; 1653.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |
| vg0221477121 | T -> C | LOC_Os02g35750.3 | downstream_gene_variant ; 1488.0bp to feature; MODIFIER | silent_mutation | Average:65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 | N | N | N | N |