| Variant ID: vg0420224622 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 20224622 |
| Reference Allele: G | Alternative Allele: GAC |
| Primary Allele: G | Secondary Allele: GAC |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )
CATCTTTCATAAAAAGACAACTGAAGCGGCAGAAGGAAGTCGGTGGCATCAAATGCAACCAAAAACAGAACAGATTCAAAGGGGTCATCCAGGCCCAGGA[G/GAC]
ACAGAGTTTGCAGAAGACCACTACTACTAAAAATTTGAAAGCCTTAAAAATACGAACAGCACAATAGATCAATTTGGGCTAAGGTTCAACCGTTTGCTGA
TCAGCAAACGGTTGAACCTTAGCCCAAATTGATCTATTGTGCTGTTCGTATTTTTAAGGCTTTCAAATTTTTAGTAGTAGTGGTCTTCTGCAAACTCTGT[C/GTC]
TCCTGGGCCTGGATGACCCCTTTGAATCTGTTCTGTTTTTGGTTGCATTTGATGCCACCGACTTCCTTCTGCCGCTTCAGTTGTCTTTTTATGAAAGATG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GAC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.00% | 8.40% | 2.75% | 57.83% | NA |
| All Indica | 2759 | 6.60% | 0.30% | 3.01% | 90.14% | NA |
| All Japonica | 1512 | 72.40% | 24.70% | 2.38% | 0.53% | NA |
| Aus | 269 | 26.00% | 0.00% | 2.60% | 71.38% | NA |
| Indica I | 595 | 3.50% | 0.00% | 2.86% | 93.61% | NA |
| Indica II | 465 | 11.20% | 0.00% | 0.65% | 88.17% | NA |
| Indica III | 913 | 4.30% | 0.10% | 5.04% | 90.58% | NA |
| Indica Intermediate | 786 | 8.90% | 0.80% | 2.16% | 88.17% | NA |
| Temperate Japonica | 767 | 71.10% | 24.30% | 4.43% | 0.26% | NA |
| Tropical Japonica | 504 | 87.10% | 11.70% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 45.60% | 53.50% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 67.70% | 8.30% | 0.00% | 23.96% | NA |
| Intermediate | 90 | 62.20% | 7.80% | 4.44% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420224622 | G -> DEL | N | N | silent_mutation | Average:63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 | N | N | N | N |
| vg0420224622 | G -> GAC | LOC_Os04g33440.2 | 3_prime_UTR_variant ; 255.0bp to feature; MODIFIER | silent_mutation | Average:63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 | N | N | N | N |
| vg0420224622 | G -> GAC | LOC_Os04g33450.1 | upstream_gene_variant ; 1549.0bp to feature; MODIFIER | silent_mutation | Average:63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 | N | N | N | N |
| vg0420224622 | G -> GAC | LOC_Os04g33450.3 | upstream_gene_variant ; 1549.0bp to feature; MODIFIER | silent_mutation | Average:63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 | N | N | N | N |
| vg0420224622 | G -> GAC | LOC_Os04g33450.2 | upstream_gene_variant ; 1541.0bp to feature; MODIFIER | silent_mutation | Average:63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 | N | N | N | N |
| vg0420224622 | G -> GAC | LOC_Os04g33430.1 | downstream_gene_variant ; 2261.0bp to feature; MODIFIER | silent_mutation | Average:63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 | N | N | N | N |
| vg0420224622 | G -> GAC | LOC_Os04g33420.1 | downstream_gene_variant ; 4599.0bp to feature; MODIFIER | silent_mutation | Average:63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 | N | N | N | N |