| Variant ID: vg0320572223 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 20572223 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele: Not determined.
AACATACAAGTCAACTTCTATTAGTTATAACAAAAATGATTTGATAAATATAATTGCCAATGTATATATGTATCTGTCTGTCAATGCAAATAGTGTATTA[TA/T]
AAAAAACTATATATTGGATATATAGGTGTGGCGATCGCTGGACGTGGAGGGGAGCTCGCCGGACCTGACCAACGGAGTGAAGCTTGGGCAGAGCATGGCG
CGCCATGCTCTGCCCAAGCTTCACTCCGTTGGTCAGGTCCGGCGAGCTCCCCTCCACGTCCAGCGATCGCCACACCTATATATCCAATATATAGTTTTTT[TA/A]
TAATACACTATTTGCATTGACAGACAGATACATATATACATTGGCAATTATATTTATCAAATCATTTTTGTTATAACTAATAGAAGTTGACTTGTATGTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.70% | 31.80% | 0.00% | 0.44% | NA |
| All Indica | 2759 | 97.60% | 2.00% | 0.00% | 0.33% | NA |
| All Japonica | 1512 | 12.90% | 86.60% | 0.00% | 0.46% | NA |
| Aus | 269 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.00% | 0.00% | 0.34% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.80% | 1.00% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 95.70% | 3.70% | 0.00% | 0.64% | NA |
| Temperate Japonica | 767 | 0.50% | 99.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 34.10% | 65.30% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 7.90% | 90.90% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 27.10% | 72.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 43.30% | 0.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0320572223 | TA -> T | LOC_Os03g37110.1 | upstream_gene_variant ; 3701.0bp to feature; MODIFIER | silent_mutation | Average:76.44; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg0320572223 | TA -> T | LOC_Os03g37130.1 | downstream_gene_variant ; 2017.0bp to feature; MODIFIER | silent_mutation | Average:76.44; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg0320572223 | TA -> T | LOC_Os03g37120.1 | intron_variant ; MODIFIER | silent_mutation | Average:76.44; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |
| vg0320572223 | TA -> DEL | N | N | silent_mutation | Average:76.44; most accessible tissue: Zhenshan97 panicle, score: 86.058 | N | N | N | N |