| Variant ID: vg0804463130 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 4463130 |
| Reference Allele: TA | Alternative Allele: T,AA,TAA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCGTATTTGATCCTAGATAGATATAGCAGATGCTTACATGGTCTAAGTAACATTCTTTGATAAGGTTTAATGCATATAAATATTGCATCAGTTTTTTTT[TA/T,AA,TAA]
AAAAAAAAATTCTTCAATTGTTGTGATATATGCGCCCCAACCGATTTGAACTCTCAATGTAGGACTAATATATTCCCGGGTATTATGTTCACCTCCATTA
TAATGGAGGTGAACATAATACCCGGGAATATATTAGTCCTACATTGAGAGTTCAAATCGGTTGGGGCGCATATATCACAACAATTGAAGAATTTTTTTTT[TA/A,TT,TTA]
AAAAAAAACTGATGCAATATTTATATGCATTAAACCTTATCAAAGAATGTTACTTAGACCATGTAAGCATCTGCTATATCTATCTAGGATCAAATACGAA
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.40% | 0.70% | 0.32% | 65.38% | TAA: 0.08%; AA: 0.08% |
| All Indica | 2759 | 4.00% | 0.50% | 0.51% | 94.89% | TAA: 0.07% |
| All Japonica | 1512 | 93.40% | 1.30% | 0.07% | 4.96% | AA: 0.26%; TAA: 0.07% |
| Aus | 269 | 3.00% | 0.00% | 0.00% | 97.03% | NA |
| Indica I | 595 | 7.20% | 0.00% | 0.84% | 91.93% | NA |
| Indica II | 465 | 6.00% | 0.20% | 0.65% | 93.12% | NA |
| Indica III | 913 | 0.40% | 0.80% | 0.33% | 98.47% | NA |
| Indica Intermediate | 786 | 4.60% | 0.80% | 0.38% | 94.02% | TAA: 0.25% |
| Temperate Japonica | 767 | 98.30% | 0.10% | 0.00% | 1.56% | NA |
| Tropical Japonica | 504 | 87.70% | 0.40% | 0.00% | 11.31% | AA: 0.60% |
| Japonica Intermediate | 241 | 89.60% | 6.60% | 0.41% | 2.49% | TAA: 0.41%; AA: 0.41% |
| VI/Aromatic | 96 | 12.50% | 1.00% | 0.00% | 85.42% | TAA: 1.04% |
| Intermediate | 90 | 40.00% | 0.00% | 0.00% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463130 | TA -> AA | LOC_Os08g07900.1 | upstream_gene_variant ; 2907.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> AA | LOC_Os08g07910.1 | upstream_gene_variant ; 2009.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> AA | LOC_Os08g07930.1 | upstream_gene_variant ; 2899.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> AA | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> TAA | LOC_Os08g07900.1 | upstream_gene_variant ; 2909.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> TAA | LOC_Os08g07910.1 | upstream_gene_variant ; 2011.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> TAA | LOC_Os08g07930.1 | upstream_gene_variant ; 2897.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> TAA | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> T | LOC_Os08g07900.1 | upstream_gene_variant ; 2908.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> T | LOC_Os08g07910.1 | upstream_gene_variant ; 2010.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> T | LOC_Os08g07930.1 | upstream_gene_variant ; 2898.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> T | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463130 | TA -> DEL | N | N | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |