| Variant ID: vg0100791115 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 791115 |
| Reference Allele: AT | Alternative Allele: A |
| Primary Allele: AT | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACACAAAACTGATCTAACCATTATGAATTAGAGGTTCCTAACAAAGTTATAGAAAGTTGTTTTCCCTTATCTTTGTTATTACTAAACTTTGATGTAAACT[AT/A]
TTTTTTTTCTTCCTTCCTTCAGGTTCACAAGTCATCCTCATTGCAGGTAATGCAGATATTCCCTGTTCTTCAAATTCTCGCCTGTCAGCAACCAAGATTT
AAATCTTGGTTGCTGACAGGCGAGAATTTGAAGAACAGGGAATATCTGCATTACCTGCAATGAGGATGACTTGTGAACCTGAAGGAAGGAAGAAAAAAAA[AT/T]
AGTTTACATCAAAGTTTAGTAATAACAAAGATAAGGGAAAACAACTTTCTATAACTTTGTTAGGAACCTCTAATTCATAATGGTTAGATCAGTTTTGTGT
| Populations | Population Size | Frequency of AT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.50% | 2.60% | 4.04% | 39.82% | NA |
| All Indica | 2759 | 50.40% | 0.30% | 3.33% | 45.99% | NA |
| All Japonica | 1512 | 63.20% | 7.50% | 4.76% | 24.54% | NA |
| Aus | 269 | 40.50% | 0.00% | 7.43% | 52.04% | NA |
| Indica I | 595 | 70.40% | 0.20% | 1.68% | 27.73% | NA |
| Indica II | 465 | 76.10% | 0.00% | 1.08% | 22.80% | NA |
| Indica III | 913 | 18.40% | 0.40% | 4.49% | 76.67% | NA |
| Indica Intermediate | 786 | 57.10% | 0.40% | 4.58% | 37.91% | NA |
| Temperate Japonica | 767 | 53.30% | 12.40% | 8.34% | 25.95% | NA |
| Tropical Japonica | 504 | 82.90% | 0.40% | 0.79% | 15.87% | NA |
| Japonica Intermediate | 241 | 53.10% | 7.10% | 1.66% | 38.17% | NA |
| VI/Aromatic | 96 | 12.50% | 0.00% | 4.17% | 83.33% | NA |
| Intermediate | 90 | 71.10% | 1.10% | 3.33% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791115 | AT -> A | LOC_Os01g02430.1 | upstream_gene_variant ; 2497.0bp to feature; MODIFIER | silent_mutation | Average:30.461; most accessible tissue: Zhenshan97 young leaf, score: 47.986 | N | N | N | N |
| vg0100791115 | AT -> A | LOC_Os01g02460.1 | upstream_gene_variant ; 3383.0bp to feature; MODIFIER | silent_mutation | Average:30.461; most accessible tissue: Zhenshan97 young leaf, score: 47.986 | N | N | N | N |
| vg0100791115 | AT -> A | LOC_Os01g02450.1 | downstream_gene_variant ; 1972.0bp to feature; MODIFIER | silent_mutation | Average:30.461; most accessible tissue: Zhenshan97 young leaf, score: 47.986 | N | N | N | N |
| vg0100791115 | AT -> A | LOC_Os01g02440.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.461; most accessible tissue: Zhenshan97 young leaf, score: 47.986 | N | N | N | N |
| vg0100791115 | AT -> DEL | N | N | silent_mutation | Average:30.461; most accessible tissue: Zhenshan97 young leaf, score: 47.986 | N | N | N | N |