| Variant ID: vg0430654714 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 30654714 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TAAACAGGAATTTAATGCGAAAACAGTTGTAATAATTAAGCAGTATTAAACATCCGCTGTCCAACGCTAACCCACGTTGCAACAGGCCCAACCATCCACC[TA/T]
AACTATCCAAGTTCAACAGATTACACTAGGGTGAGACTAATCACGGTGAATCTGGTTGACCGCCCATAACCGCGGGCACGGCTATTCGAATAGTTTTACT
AGTAAAACTATTCGAATAGCCGTGCCCGCGGTTATGGGCGGTCAACCAGATTCACCGTGATTAGTCTCACCCTAGTGTAATCTGTTGAACTTGGATAGTT[TA/A]
GGTGGATGGTTGGGCCTGTTGCAACGTGGGTTAGCGTTGGACAGCGGATGTTTAATACTGCTTAATTATTACAACTGTTTTCGCATTAAATTCCTGTTTA
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 4.20% | 0.30% | 38.30% | 57.24% | NA |
| All Indica | 2759 | 0.30% | 0.00% | 42.62% | 57.09% | NA |
| All Japonica | 1512 | 12.50% | 0.70% | 22.95% | 63.82% | NA |
| Aus | 269 | 0.00% | 0.00% | 68.03% | 31.97% | NA |
| Indica I | 595 | 0.00% | 0.00% | 20.50% | 79.50% | NA |
| Indica II | 465 | 0.90% | 0.00% | 43.44% | 55.70% | NA |
| Indica III | 913 | 0.10% | 0.00% | 60.79% | 39.10% | NA |
| Indica Intermediate | 786 | 0.40% | 0.00% | 37.79% | 61.83% | NA |
| Temperate Japonica | 767 | 18.50% | 0.30% | 17.60% | 63.62% | NA |
| Tropical Japonica | 504 | 3.60% | 0.80% | 30.56% | 65.08% | NA |
| Japonica Intermediate | 241 | 12.00% | 2.10% | 24.07% | 61.83% | NA |
| VI/Aromatic | 96 | 0.00% | 1.00% | 58.33% | 40.62% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 53.33% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654714 | TA -> DEL | N | N | silent_mutation | Average:5.888; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg0430654714 | TA -> T | LOC_Os04g51720.1 | downstream_gene_variant ; 2317.0bp to feature; MODIFIER | silent_mutation | Average:5.888; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg0430654714 | TA -> T | LOC_Os04g51740.1 | downstream_gene_variant ; 2664.0bp to feature; MODIFIER | silent_mutation | Average:5.888; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |
| vg0430654714 | TA -> T | LOC_Os04g51730.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.888; most accessible tissue: Minghui63 flag leaf, score: 11.122 | N | N | N | N |