| Variant ID: vg0400681203 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 681203 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 268. )
TTTACTTCTTTTCCAACCACTGTTGAGTAACCACGTCTTTCGACGTATGCGGTTGTCGTTTCGACAATACTATTATAAACTAAAAGTTCAGTACATTTCC[T/TA]
AAAAAACACTCGTACACCATCACATGATACCTTCTAAAATCAGAGAAATCCTCGAAATTCTAAAAAAAAAATCTGACCATCAACTATCATTTAAACCGAC
GTCGGTTTAAATGATAGTTGATGGTCAGATTTTTTTTTTAGAATTTCGAGGATTTCTCTGATTTTAGAAGGTATCATGTGATGGTGTACGAGTGTTTTTT[A/TA]
GGAAATGTACTGAACTTTTAGTTTATAATAGTATTGTCGAAACGACAACCGCATACGTCGAAAGACGTGGTTACTCAACAGTGGTTGGAAAAGAAGTAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.60% | 2.80% | 0.61% | 1.04% | NA |
| All Indica | 2759 | 93.70% | 4.20% | 0.40% | 1.74% | NA |
| All Japonica | 1512 | 98.70% | 0.10% | 1.12% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.60% | 0.90% | 0.65% | 6.88% | NA |
| Indica III | 913 | 91.30% | 7.80% | 0.77% | 0.11% | NA |
| Indica Intermediate | 786 | 94.10% | 3.80% | 0.13% | 1.91% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 96.40% | 0.00% | 3.37% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 11.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0400681203 | T -> DEL | N | N | silent_mutation | Average:78.932; most accessible tissue: Minghui63 flag leaf, score: 87.461 | N | N | N | N |
| vg0400681203 | T -> TA | LOC_Os04g02110.1 | 3_prime_UTR_variant ; 3087.0bp to feature; MODIFIER | silent_mutation | Average:78.932; most accessible tissue: Minghui63 flag leaf, score: 87.461 | N | N | N | N |
| vg0400681203 | T -> TA | LOC_Os04g02110.3 | 3_prime_UTR_variant ; 3087.0bp to feature; MODIFIER | silent_mutation | Average:78.932; most accessible tissue: Minghui63 flag leaf, score: 87.461 | N | N | N | N |
| vg0400681203 | T -> TA | LOC_Os04g02090.1 | upstream_gene_variant ; 4540.0bp to feature; MODIFIER | silent_mutation | Average:78.932; most accessible tissue: Minghui63 flag leaf, score: 87.461 | N | N | N | N |
| vg0400681203 | T -> TA | LOC_Os04g02100.1 | downstream_gene_variant ; 216.0bp to feature; MODIFIER | silent_mutation | Average:78.932; most accessible tissue: Minghui63 flag leaf, score: 87.461 | N | N | N | N |
| vg0400681203 | T -> TA | LOC_Os04g02110.2 | downstream_gene_variant ; 2501.0bp to feature; MODIFIER | silent_mutation | Average:78.932; most accessible tissue: Minghui63 flag leaf, score: 87.461 | N | N | N | N |