| Variant ID: vg0132053897 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 32053897 |
| Reference Allele: T | Alternative Allele: TAA,TA,TAAA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 300. )
CAGAAGTTTCCAATTCTTAATCTTCTACAAATGAGTGCCGTGAAAGTAAATTTGTACCAGGTAAAATCACAAGATATATTATCTTAGCAAAGAAAAGCTT[T/TAA,TA,TAAA]
AAAAAATATGCTGACAACTTTTTATAATATTTTTGTTGTAGAACGCGCTCCTTTCACCTTTTTGGAACATCAATGCTCATAGCATTGTCTATATTACTCA
TGAGTAATATAGACAATGCTATGAGCATTGATGTTCCAAAAAGGTGAAAGGAGCGCGTTCTACAACAAAAATATTATAAAAAGTTGTCAGCATATTTTTT[A/TTA,TA,TTTA]
AAGCTTTTCTTTGCTAAGATAATATATCTTGTGATTTTACCTGGTACAAATTTACTTTCACGGCACTCATTTGTAGAAGATTAAGAATTGGAAACTTCTG
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.10% | 24.00% | 0.40% | 0.00% | TAA: 15.47%; TAAA: 0.04% |
| All Indica | 2759 | 74.80% | 1.90% | 0.43% | 0.00% | TAA: 22.80%; TAAA: 0.07% |
| All Japonica | 1512 | 30.70% | 69.20% | 0.07% | 0.00% | NA |
| Aus | 269 | 61.70% | 0.40% | 1.86% | 0.00% | TAA: 36.06% |
| Indica I | 595 | 53.60% | 3.00% | 1.01% | 0.00% | TAA: 42.35% |
| Indica II | 465 | 98.70% | 1.10% | 0.00% | 0.00% | TAA: 0.22% |
| Indica III | 913 | 74.70% | 0.00% | 0.11% | 0.00% | TAA: 24.97%; TAAA: 0.22% |
| Indica Intermediate | 786 | 76.70% | 3.80% | 0.64% | 0.00% | TAA: 18.83% |
| Temperate Japonica | 767 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 84.70% | 15.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 12.00% | 87.60% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 26.70% | 1.11% | 0.00% | TAA: 5.56% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0132053897 | T -> TA | LOC_Os01g55620.1 | upstream_gene_variant ; 3132.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TA | LOC_Os01g55640.1 | upstream_gene_variant ; 3257.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TA | LOC_Os01g55650.1 | downstream_gene_variant ; 3485.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TA | LOC_Os01g55630.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAAA | LOC_Os01g55620.1 | upstream_gene_variant ; 3132.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAAA | LOC_Os01g55640.1 | upstream_gene_variant ; 3257.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAAA | LOC_Os01g55650.1 | downstream_gene_variant ; 3485.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAAA | LOC_Os01g55630.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAA | LOC_Os01g55620.1 | upstream_gene_variant ; 3132.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAA | LOC_Os01g55640.1 | upstream_gene_variant ; 3257.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAA | LOC_Os01g55650.1 | downstream_gene_variant ; 3485.0bp to feature; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg0132053897 | T -> TAA | LOC_Os01g55630.1 | intron_variant ; MODIFIER | silent_mutation | Average:44.552; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |