| Variant ID: vg0724212549 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 24212549 |
| Reference Allele: G | Alternative Allele: GT |
| Primary Allele: G | Secondary Allele: GT |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )
TATCGTCCAGTTCTAGTGGTTCTTCAGTAGTTTCCTAGCTAACTTTCGGGTCCTTAGTTATCATCAGACATAGGTGTCTATCGTCTATCAGTATTTTAGT[G/GT]
TTCTAGCTTTATTATCCATGTAACTCTGGAGTGATGAGGGAACAGCATGTCGATCCTGGCATCTTCAGGTGTAGGTTCTCTAGTAGGTTCAGATCGAATC
GATTCGATCTGAACCTACTAGAGAACCTACACCTGAAGATGCCAGGATCGACATGCTGTTCCCTCATCACTCCAGAGTTACATGGATAATAAAGCTAGAA[C/AC]
ACTAAAATACTGATAGACGATAGACACCTATGTCTGATGATAACTAAGGACCCGAAAGTTAGCTAGGAAACTACTGAAGAACCACTAGAACTGGACGATA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.80% | 20.90% | 0.08% | 0.21% | NA |
| All Indica | 2759 | 95.00% | 4.90% | 0.04% | 0.14% | NA |
| All Japonica | 1512 | 49.00% | 50.70% | 0.20% | 0.13% | NA |
| Aus | 269 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.00% | 8.60% | 0.22% | 0.22% | NA |
| Indica III | 913 | 97.70% | 2.10% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 94.00% | 5.90% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 85.00% | 14.70% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 6.70% | 93.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 22.80% | 75.90% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 50.00% | 49.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 68.90% | 27.80% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0724212549 | G -> DEL | N | N | silent_mutation | Average:76.948; most accessible tissue: Callus, score: 99.911 | N | N | N | N |
| vg0724212549 | G -> GT | LOC_Os07g40380.1 | 3_prime_UTR_variant ; 208.0bp to feature; MODIFIER | silent_mutation | Average:76.948; most accessible tissue: Callus, score: 99.911 | N | N | N | N |
| vg0724212549 | G -> GT | LOC_Os07g40370.1 | upstream_gene_variant ; 4585.0bp to feature; MODIFIER | silent_mutation | Average:76.948; most accessible tissue: Callus, score: 99.911 | N | N | N | N |
| vg0724212549 | G -> GT | LOC_Os07g40390.1 | downstream_gene_variant ; 3328.0bp to feature; MODIFIER | silent_mutation | Average:76.948; most accessible tissue: Callus, score: 99.911 | N | N | N | N |