| Variant ID: vg0424199537 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 24199537 |
| Reference Allele: C | Alternative Allele: CAAA,CAA,CA |
| Primary Allele: C | Secondary Allele: CAAA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 250. )
TTGCTCTTCTTGCAGATCACGAATCTCTTTATCAGCTCTTCCTCAACGGGTACACAGAGATGGTCCGTTGCCTACACAAATATAGCATTTTAGTGATTAA[C/CAAA,CAA,CA]
AAAAAAAAAGTTGAAAGAAGAGACAACGATGAATATCCGTACACTACCTATGGTTATAAATAAGCTTTCTGTTAGATAAGTTTTAGAAAAAATCTACTAA
TTAGTAGATTTTTTCTAAAACTTATCTAACAGAAAGCTTATTTATAACCATAGGTAGTGTACGGATATTCATCGTTGTCTCTTCTTTCAACTTTTTTTTT[G/TTTG,TTG,TG]
TTAATCACTAAAATGCTATATTTGTGTAGGCAACGGACCATCTCTGTGTACCCGTTGAGGAAGAGCTGATAAAGAGATTCGTGATCTGCAAGAAGAGCAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.10% | 4.40% | 13.94% | 18.39% | CA: 0.13%; CAA: 0.04% |
| All Indica | 2759 | 41.60% | 5.00% | 23.38% | 29.94% | CA: 0.14% |
| All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 59.90% | 24.90% | 2.23% | 12.27% | CAA: 0.74% |
| Indica I | 595 | 14.50% | 0.00% | 42.52% | 43.03% | NA |
| Indica II | 465 | 86.90% | 1.10% | 3.66% | 7.74% | CA: 0.65% |
| Indica III | 913 | 34.70% | 9.50% | 23.66% | 31.98% | CA: 0.11% |
| Indica Intermediate | 786 | 43.30% | 5.70% | 20.23% | 30.79% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 6.67% | 11.11% | CA: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424199537 | C -> CA | LOC_Os04g40770.1 | downstream_gene_variant ; 4188.0bp to feature; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CA | LOC_Os04g40790.1 | downstream_gene_variant ; 2775.0bp to feature; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CA | LOC_Os04g40780.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CAAA | LOC_Os04g40770.1 | downstream_gene_variant ; 4188.0bp to feature; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CAAA | LOC_Os04g40790.1 | downstream_gene_variant ; 2775.0bp to feature; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CAAA | LOC_Os04g40780.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> DEL | N | N | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CAA | LOC_Os04g40770.1 | downstream_gene_variant ; 4188.0bp to feature; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CAA | LOC_Os04g40790.1 | downstream_gene_variant ; 2775.0bp to feature; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199537 | C -> CAA | LOC_Os04g40780.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.991; most accessible tissue: Callus, score: 76.576 | N | N | N | N |