| Variant ID: vg0114587401 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 14587401 |
| Reference Allele: T | Alternative Allele: TC,C,TTC |
| Primary Allele: T | Secondary Allele: TC |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, TC: 0.02, others allele: 0.00, population size: 177. )
AATCAATTCTACTGCTTTATGCATAAAAATTGTTTAAGCATCTCAATGTATCAAATGTTAACCAAAACTAAACTGAAGCGGTTAAATAAGCTTTTTTTTT[T/TC,C,TTC]
ATTGCTGAAGAGTACATTAATTTAAGTGTTGCATTCATGGTAAGAACAAGAACAACTATACAGAGTTTTTGTATGTACGAAGTTGAGTACTCACATATGT
ACATATGTGAGTACTCAACTTCGTACATACAAAAACTCTGTATAGTTGTTCTTGTTCTTACCATGAATGCAACACTTAAATTAATGTACTCTTCAGCAAT[A/GA,G,GAA]
AAAAAAAAAGCTTATTTAACCGCTTCAGTTTAGTTTTGGTTAACATTTGATACATTGAGATGCTTAAACAATTTTTATGCATAAAGCAGTAGAATTGATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.70% | 17.90% | 0.57% | 20.82% | C: 0.04% |
| All Indica | 2759 | 34.00% | 29.90% | 0.98% | 35.05% | C: 0.07% |
| All Japonica | 1512 | 99.70% | 0.10% | 0.00% | 0.20% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 42.00% | 6.70% | 0.67% | 50.59% | NA |
| Indica II | 465 | 23.00% | 46.20% | 0.43% | 30.32% | NA |
| Indica III | 913 | 33.80% | 36.30% | 0.88% | 28.92% | C: 0.11% |
| Indica Intermediate | 786 | 34.50% | 30.50% | 1.65% | 33.21% | C: 0.13% |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 16.70% | 0.00% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587401 | T -> TC | LOC_Os01g25730.1 | downstream_gene_variant ; 4024.0bp to feature; MODIFIER | silent_mutation | Average:62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |
| vg0114587401 | T -> TC | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |
| vg0114587401 | T -> DEL | N | N | silent_mutation | Average:62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |
| vg0114587401 | T -> C | LOC_Os01g25730.1 | downstream_gene_variant ; 4023.0bp to feature; MODIFIER | silent_mutation | Average:62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |
| vg0114587401 | T -> C | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |
| vg0114587401 | T -> TTC | LOC_Os01g25730.1 | downstream_gene_variant ; 4024.0bp to feature; MODIFIER | N | Average:62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |
| vg0114587401 | T -> TTC | LOC_Os01g25740.1 | intron_variant ; MODIFIER | N | Average:62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 | N | N | N | N |