| Variant ID: vg0204059008 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 4059008 |
| Reference Allele: TGTAGTTATGGTAATAATTAA | Alternative Allele: T |
| Primary Allele: TGTAGTTATGGTAATAATTA A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCCAATTTTAATTTGTTGGACAATTCAAATTGTCCATATATATGCATGATGATGAGCTTTGCTAATTAGGGCATAATTATTAGCCTAATTAACTAATCT[TGTAGTTATGGTAATAATTAA/T]
GTAGTATAAGTAAAGGTTCATGAGAATGTTGAGGTATGTAATTTAAGTTGTTGATGTATGCATGATGAGAAGCTAAGCTGGCTGTATGTATGCATGGCAG
CTGCCATGCATACATACAGCCAGCTTAGCTTCTCATCATGCATACATCAACAACTTAAATTACATACCTCAACATTCTCATGAACCTTTACTTATACTAC[TTAATTATTACCATAACTACA/A]
AGATTAGTTAATTAGGCTAATAATTATGCCCTAATTAGCAAAGCTCATCATCATGCATATATATGGACAATTTGAATTGTCCAACAAATTAAAATTGGGC
| Populations | Population Size | Frequency of TGTAGTTATGGTAATAATTA A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.50% | 40.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0204059008 | TGTAGTTATGGTAATAATTAA -> T | LOC_Os02g07770.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.034; most accessible tissue: Callus, score: 74.473 | N | N | N | N |