| Variant ID: vg0100790572 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 790572 |
| Reference Allele: AT | Alternative Allele: ATT,ATTT,A,ATTTT |
| Primary Allele: AT | Secondary Allele: ATTT |
Inferred Ancestral Allele: Not determined.
CCAATGCTTGTCAGGGGTGTGAGTGGAATGGTCATCACTGCGGATTTAGTTCACAAAGGGGCCAGGCATTCTGCCAGCATCAAGGTATCCTTCATCTCAT[AT/ATT,ATTT,A,ATTTT]
TTTTTTTTCACAAGGGAATTCTACAAGTTATTTCTTCTATTTATTGTATTAATAATTATGTTATGGAATTCATAATTATCAAGCTTTTTTTAAACAATTC
GAATTGTTTAAAAAAAGCTTGATAATTATGAATTCCATAACATAATTATTAATACAATAAATAGAAGAAATAACTTGTAGAATTCCCTTGTGAAAAAAAA[AT/AAT,AAAT,T,AAAAT]
ATGAGATGAAGGATACCTTGATGCTGGCAGAATGCCTGGCCCCTTTGTGAACTAAATCCGCAGTGATGACCATTCCACTCACACCCCTGACAAGCATTGG
| Populations | Population Size | Frequency of AT(primary allele) | Frequency of ATTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.80% | 10.00% | 4.55% | 42.89% | ATT: 9.65%; A: 0.11%; ATTTT: 0.02% |
| All Indica | 2759 | 27.60% | 3.70% | 5.98% | 48.97% | ATT: 13.59%; A: 0.14% |
| All Japonica | 1512 | 44.00% | 23.10% | 2.12% | 26.59% | ATT: 4.10%; ATTTT: 0.07% |
| Aus | 269 | 31.20% | 0.40% | 2.23% | 62.08% | ATT: 3.72%; A: 0.37% |
| Indica I | 595 | 1.80% | 12.10% | 16.13% | 30.92% | ATT: 38.99% |
| Indica II | 465 | 71.20% | 1.10% | 1.08% | 23.66% | ATT: 3.01% |
| Indica III | 913 | 14.50% | 0.70% | 1.64% | 80.50% | ATT: 2.30%; A: 0.44% |
| Indica Intermediate | 786 | 36.50% | 2.50% | 6.23% | 40.97% | ATT: 13.74% |
| Temperate Japonica | 767 | 68.10% | 1.60% | 0.91% | 29.07% | ATT: 0.39% |
| Tropical Japonica | 504 | 5.80% | 62.70% | 3.97% | 16.67% | ATT: 10.71%; ATTTT: 0.20% |
| Japonica Intermediate | 241 | 47.70% | 8.70% | 2.07% | 39.42% | ATT: 2.07% |
| VI/Aromatic | 96 | 4.20% | 5.20% | 5.21% | 84.38% | ATT: 1.04% |
| Intermediate | 90 | 40.00% | 14.40% | 7.78% | 28.89% | ATT: 8.89% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100790572 | AT -> A | LOC_Os01g02430.1 | upstream_gene_variant ; 1954.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> A | LOC_Os01g02460.1 | upstream_gene_variant ; 3926.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> A | LOC_Os01g02450.1 | downstream_gene_variant ; 2515.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> A | LOC_Os01g02440.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATT | LOC_Os01g02430.1 | upstream_gene_variant ; 1955.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATT | LOC_Os01g02460.1 | upstream_gene_variant ; 3925.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATT | LOC_Os01g02450.1 | downstream_gene_variant ; 2514.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATT | LOC_Os01g02440.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTT | LOC_Os01g02430.1 | upstream_gene_variant ; 1955.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTT | LOC_Os01g02460.1 | upstream_gene_variant ; 3925.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTT | LOC_Os01g02450.1 | downstream_gene_variant ; 2514.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTT | LOC_Os01g02440.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTTT | LOC_Os01g02430.1 | upstream_gene_variant ; 1955.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTTT | LOC_Os01g02460.1 | upstream_gene_variant ; 3925.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTTT | LOC_Os01g02450.1 | downstream_gene_variant ; 2514.0bp to feature; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> ATTTT | LOC_Os01g02440.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |
| vg0100790572 | AT -> DEL | N | N | silent_mutation | Average:35.988; most accessible tissue: Callus, score: 77.623 | N | N | N | N |