| Variant ID: vg0137237215 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 37237215 |
| Reference Allele: GTT | Alternative Allele: G,GTTT |
| Primary Allele: G | Secondary Allele: GTT |
Inferred Ancestral Allele: Not determined.
CCGTAGCTTACCATTGCCCCCAGTTTAATTTCATTCGTTCGCCACTGTCGTTTATATGAAGAATAAAAAAAGGTGACCATTTGTTGCAGCTTAAATTGAT[GTT/G,GTTT]
TTTTTTGAGAGAGAGATTAGTTGATGTTTTGAGAGAACATAAATATGCGAGCATTTCCTGCTTGAAAATAATATTCATTTCTATATGAAAACAGGACAAT
ATTGTCCTGTTTTCATATAGAAATGAATATTATTTTCAAGCAGGAAATGCTCGCATATTTATGTTCTCTCAAAACATCAACTAATCTCTCTCTCAAAAAA[AAC/C,AAAC]
ATCAATTTAAGCTGCAACAAATGGTCACCTTTTTTTATTCTTCATATAAACGACAGTGGCGAACGAATGAAATTAAACTGGGGGCAATGGTAAGCTACGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.60% | 35.20% | 0.13% | 0.00% | GTTT: 0.11% |
| All Indica | 2759 | 98.30% | 1.60% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 2.10% | 97.40% | 0.13% | 0.00% | GTTT: 0.33% |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.20% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.70% | 4.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 1.60% | 98.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 3.00% | 96.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 95.90% | 0.00% | 0.00% | GTTT: 2.07% |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 42.20% | 57.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137237215 | GTT -> G | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 397.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |
| vg0137237215 | GTT -> G | LOC_Os01g64110.1 | upstream_gene_variant ; 1685.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |
| vg0137237215 | GTT -> G | LOC_Os01g64120.1 | upstream_gene_variant ; 3939.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |
| vg0137237215 | GTT -> G | LOC_Os01g64090.1 | downstream_gene_variant ; 2841.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |
| vg0137237215 | GTT -> GTTT | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 399.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |
| vg0137237215 | GTT -> GTTT | LOC_Os01g64110.1 | upstream_gene_variant ; 1683.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |
| vg0137237215 | GTT -> GTTT | LOC_Os01g64120.1 | upstream_gene_variant ; 3937.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |
| vg0137237215 | GTT -> GTTT | LOC_Os01g64090.1 | downstream_gene_variant ; 2843.0bp to feature; MODIFIER | silent_mutation | Average:55.155; most accessible tissue: Callus, score: 81.176 | N | N | N | N |