| Variant ID: vg1023166415 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 23166415 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 368. )
ATAAAGGCAAGGTCGAGTTCTCTTTTCCATTCTTCGTAGTTATCTCCTTTCAGGGTCGGAATATCTTTAATGTAACCCATCAAGGAGTAGCCACCTGAGA[T/A]
AATCATGTATTGTGAGAACAAAATTAACATTAAAATTATTATGTATTAAGTCTACATCACCGTTGGGCAGAAAATAGACATAACACATAAAGCCATAACT
AGTTATGGCTTTATGTGTTATGTCTATTTTCTGCCCAACGGTGATGTAGACTTAATACATAATAATTTTAATGTTAATTTTGTTCTCACAATACATGATT[A/T]
TCTCAGGTGGCTACTCCTTGATGGGTTACATTAAAGATATTCCGACCCTGAAAGGAGATAACTACGAAGAATGGAAAAGAGAACTCGACCTTGCCTTTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.80% | 1.00% | 0.85% | 12.42% | NA |
| All Indica | 2759 | 77.30% | 1.30% | 1.38% | 20.04% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Aus | 269 | 87.70% | 3.30% | 0.74% | 8.18% | NA |
| Indica I | 595 | 61.00% | 0.00% | 2.52% | 36.47% | NA |
| Indica II | 465 | 71.00% | 0.40% | 0.43% | 28.17% | NA |
| Indica III | 913 | 90.50% | 3.40% | 0.99% | 5.15% | NA |
| Indica Intermediate | 786 | 78.00% | 0.40% | 1.53% | 20.10% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 1.10% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1023166415 | T -> A | LOC_Os10g42980.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166415 | T -> A | LOC_Os10g42970.1 | upstream_gene_variant ; 4000.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166415 | T -> A | LOC_Os10g42999.1 | upstream_gene_variant ; 3038.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166415 | T -> A | LOC_Os10g42970.2 | upstream_gene_variant ; 4000.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1023166415 | T -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |