| Variant ID: vg0203137495 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 3137495 |
| Reference Allele: GT | Alternative Allele: G,GTT |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAGTCTGCCCAGTTTCAGGGTTTCTCCCCCTCCAGTCGGAGGCTGTGCCTCGGACCATGCTCGACATGCTTTTGTCGATGTAACTATACTTTTGTACTTT[GT/G,GTT]
TTTTTTTTTACTAATTCTTAATGAAATTGGTTGGCCACTCTTTGGCTGACCCGGCAAAAACGAGGGACTTCAGGTTGTCTATTCTTGGTGACAACTGGCC
GGCCAGTTGTCACCAAGAATAGACAACCTGAAGTCCCTCGTTTTTGCCGGGTCAGCCAAAGAGTGGCCAACCAATTTCATTAAGAATTAGTAAAAAAAAA[AC/C,AAC]
AAAGTACAAAAGTATAGTTACATCGACAAAAGCATGTCGAGCATGGTCCGAGGCACAGCCTCCGACTGGAGGGGGAGAAACCCTGAAACTGGGCAGACTA
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.30% | 14.30% | 0.38% | 1.95% | GTT: 0.04% |
| All Indica | 2759 | 73.40% | 24.00% | 0.11% | 2.46% | GTT: 0.04% |
| All Japonica | 1512 | 99.30% | 0.50% | 0.07% | 0.13% | NA |
| Aus | 269 | 98.50% | 0.70% | 0.00% | 0.37% | GTT: 0.37% |
| Indica I | 595 | 77.50% | 22.40% | 0.17% | 0.00% | NA |
| Indica II | 465 | 84.50% | 15.30% | 0.22% | 0.00% | NA |
| Indica III | 913 | 67.60% | 28.00% | 0.00% | 4.27% | GTT: 0.11% |
| Indica Intermediate | 786 | 70.50% | 25.70% | 0.13% | 3.69% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 68.80% | 1.00% | 14.58% | 15.62% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203137495 | GT -> G | LOC_Os02g06270.1 | upstream_gene_variant ; 2511.0bp to feature; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> G | LOC_Os02g06290.1 | upstream_gene_variant ; 4496.0bp to feature; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> G | LOC_Os02g06290.2 | upstream_gene_variant ; 4798.0bp to feature; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> G | LOC_Os02g06280.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> GTT | LOC_Os02g06270.1 | upstream_gene_variant ; 2512.0bp to feature; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> GTT | LOC_Os02g06290.1 | upstream_gene_variant ; 4495.0bp to feature; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> GTT | LOC_Os02g06290.2 | upstream_gene_variant ; 4797.0bp to feature; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> GTT | LOC_Os02g06280.1 | intron_variant ; MODIFIER | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |
| vg0203137495 | GT -> DEL | N | N | silent_mutation | Average:63.366; most accessible tissue: Callus, score: 83.704 | N | N | N | N |