| Variant ID: vg0420224655 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 20224655 |
| Reference Allele: A | Alternative Allele: ATTGCAG |
| Primary Allele: ATTGCAG | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 295. )
AGGAAGTCGGTGGCATCAAATGCAACCAAAAACAGAACAGATTCAAAGGGGTCATCCAGGCCCAGGAGACAGAGTTTGCAGAAGACCACTACTACTAAAA[A/ATTGCAG]
TTTGAAAGCCTTAAAAATACGAACAGCACAATAGATCAATTTGGGCTAAGGTTCAACCGTTTGCTGAAATAAGTTGTCCAATAACGGAGAATCACTATAT
ATATAGTGATTCTCCGTTATTGGACAACTTATTTCAGCAAACGGTTGAACCTTAGCCCAAATTGATCTATTGTGCTGTTCGTATTTTTAAGGCTTTCAAA[T/CTGCAAT]
TTTTAGTAGTAGTGGTCTTCTGCAAACTCTGTCTCCTGGGCCTGGATGACCCCTTTGAATCTGTTCTGTTTTTGGTTGCATTTGATGCCACCGACTTCCT
| Populations | Population Size | Frequency of ATTGCAG(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.90% | 37.50% | 0.04% | 0.55% | NA |
| All Indica | 2759 | 94.90% | 4.60% | 0.07% | 0.43% | NA |
| All Japonica | 1512 | 3.20% | 96.40% | 0.00% | 0.33% | NA |
| Aus | 269 | 75.10% | 24.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 0.70% | 0.00% | 0.67% | NA |
| Indica II | 465 | 90.80% | 8.60% | 0.00% | 0.65% | NA |
| Indica III | 913 | 97.20% | 2.70% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 91.90% | 7.40% | 0.25% | 0.51% | NA |
| Temperate Japonica | 767 | 5.50% | 94.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.20% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 0.40% | 98.80% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 25.00% | 74.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 34.40% | 56.70% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420224655 | A -> DEL | N | N | silent_mutation | Average:64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0420224655 | A -> ATTGCAG | LOC_Os04g33440.2 | 3_prime_UTR_variant ; 222.0bp to feature; MODIFIER | silent_mutation | Average:64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0420224655 | A -> ATTGCAG | LOC_Os04g33450.1 | upstream_gene_variant ; 1582.0bp to feature; MODIFIER | silent_mutation | Average:64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0420224655 | A -> ATTGCAG | LOC_Os04g33450.3 | upstream_gene_variant ; 1582.0bp to feature; MODIFIER | silent_mutation | Average:64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0420224655 | A -> ATTGCAG | LOC_Os04g33450.2 | upstream_gene_variant ; 1574.0bp to feature; MODIFIER | silent_mutation | Average:64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0420224655 | A -> ATTGCAG | LOC_Os04g33430.1 | downstream_gene_variant ; 2228.0bp to feature; MODIFIER | silent_mutation | Average:64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0420224655 | A -> ATTGCAG | LOC_Os04g33420.1 | downstream_gene_variant ; 4566.0bp to feature; MODIFIER | silent_mutation | Average:64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |