| Variant ID: vg0703429514 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 3429514 |
| Reference Allele: GC | Alternative Allele: G |
| Primary Allele: GC | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCTATAATTTTTTTTAAAAAAACACATTATTTAGCTATTCGGAAAATACGCACGTGGAAAACAAGATTGGTGAAATTGGCAACATTGACTTTAGAACACA[GC/G]
CCAAGGCATTAACCCACCAACATCCGGGGACACGATCTTGAGTTGAGTTTCCTACTGACGACAAGTTAATGCCAACTACAGTACTAATCAGAATCTCCAT
ATGGAGATTCTGATTAGTACTGTAGTTGGCATTAACTTGTCGTCAGTAGGAAACTCAACTCAAGATCGTGTCCCCGGATGTTGGTGGGTTAATGCCTTGG[GC/C]
TGTGTTCTAAAGTCAATGTTGCCAATTTCACCAATCTTGTTTTCCACGTGCGTATTTTCCGAATAGCTAAATAATGTGTTTTTTTAAAAAAAATTATAGG
| Populations | Population Size | Frequency of GC(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.00% | 43.60% | 0.06% | 0.36% | NA |
| All Indica | 2759 | 35.80% | 63.60% | 0.07% | 0.51% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 84.70% | 15.00% | 0.00% | 0.34% | NA |
| Indica II | 465 | 15.10% | 84.10% | 0.00% | 0.86% | NA |
| Indica III | 913 | 16.00% | 83.70% | 0.00% | 0.33% | NA |
| Indica Intermediate | 786 | 34.00% | 65.10% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 34.40% | 1.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0703429514 | GC -> DEL | N | N | silent_mutation | Average:69.421; most accessible tissue: Callus, score: 93.643 | N | N | N | N |
| vg0703429514 | GC -> G | LOC_Os07g06970.1 | 3_prime_UTR_variant ; 160.0bp to feature; MODIFIER | silent_mutation | Average:69.421; most accessible tissue: Callus, score: 93.643 | N | N | N | N |
| vg0703429514 | GC -> G | LOC_Os07g06960.1 | upstream_gene_variant ; 1048.0bp to feature; MODIFIER | silent_mutation | Average:69.421; most accessible tissue: Callus, score: 93.643 | N | N | N | N |