| Variant ID: vg0724212377 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 24212377 |
| Reference Allele: AGAG | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: AGAG |
Inferred Ancestral Allele: Not determined.
TGTTATATACTATATGTTTCTTTTCTCAGAGGCCATTGAGGCAGGTTGGCTTGACTGCCTTCGAGTAGTAGGTCGTCTCTACGTCCGCGCGTTGCCGCCA[AGAG/A]
GAGGAGCTCGAGGTTCTGTGGTTGGACAAGCGTCAAGAGGTGACGTGCGGTGCGGAGGGCCTACCATGTATCGTCCAGTTCTAGTGGTTCTTCAGTAGTT
AACTACTGAAGAACCACTAGAACTGGACGATACATGGTAGGCCCTCCGCACCGCACGTCACCTCTTGACGCTTGTCCAACCACAGAACCTCGAGCTCCTC[CTCT/T]
TGGCGGCAACGCGCGGACGTAGAGACGACCTACTACTCGAAGGCAGTCAAGCCAACCTGCCTCAATGGCCTCTGAGAAAAGAAACATATAGTATATAACA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AGAG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.70% | 40.90% | 0.13% | 0.34% | NA |
| All Indica | 2759 | 91.80% | 7.70% | 0.14% | 0.33% | NA |
| All Japonica | 1512 | 0.70% | 99.10% | 0.00% | 0.20% | NA |
| Aus | 269 | 51.70% | 48.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.90% | 6.60% | 0.17% | 0.34% | NA |
| Indica II | 465 | 88.00% | 11.60% | 0.00% | 0.43% | NA |
| Indica III | 913 | 97.00% | 2.70% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 87.30% | 12.00% | 0.38% | 0.38% | NA |
| Temperate Japonica | 767 | 0.70% | 99.20% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.50% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 49.00% | 50.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 45.60% | 48.90% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724212377 | AGAG -> DEL | N | N | silent_mutation | Average:70.296; most accessible tissue: Callus, score: 98.341 | N | N | N | N |
| vg0724212377 | AGAG -> A | LOC_Os07g40380.1 | 3_prime_UTR_variant ; 40.0bp to feature; MODIFIER | silent_mutation | Average:70.296; most accessible tissue: Callus, score: 98.341 | N | N | N | N |
| vg0724212377 | AGAG -> A | LOC_Os07g40370.1 | upstream_gene_variant ; 4413.0bp to feature; MODIFIER | silent_mutation | Average:70.296; most accessible tissue: Callus, score: 98.341 | N | N | N | N |
| vg0724212377 | AGAG -> A | LOC_Os07g40390.1 | downstream_gene_variant ; 3500.0bp to feature; MODIFIER | silent_mutation | Average:70.296; most accessible tissue: Callus, score: 98.341 | N | N | N | N |