| Variant ID: vg0424199521 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 24199521 |
| Reference Allele: G | Alternative Allele: GCA |
| Primary Allele: G | Secondary Allele: GCA |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 241. )
TGGTTCCCAGTTTATATTGCTCTTCTTGCAGATCACGAATCTCTTTATCAGCTCTTCCTCAACGGGTACACAGAGATGGTCCGTTGCCTACACAAATATA[G/GCA]
CATTTTAGTGATTAACAAAAAAAAAGTTGAAAGAAGAGACAACGATGAATATCCGTACACTACCTATGGTTATAAATAAGCTTTCTGTTAGATAAGTTTT
AAAACTTATCTAACAGAAAGCTTATTTATAACCATAGGTAGTGTACGGATATTCATCGTTGTCTCTTCTTTCAACTTTTTTTTTGTTAATCACTAAAATG[C/TGC]
TATATTTGTGTAGGCAACGGACCATCTCTGTGTACCCGTTGAGGAAGAGCTGATAAAGAGATTCGTGATCTGCAAGAAGAGCAATATAAACTGGGAACCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GCA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.20% | 40.70% | 0.21% | 1.90% | NA |
| All Indica | 2759 | 31.90% | 65.70% | 0.25% | 2.17% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.10% | 30.50% | 1.12% | 9.29% | NA |
| Indica I | 595 | 4.70% | 93.90% | 0.00% | 1.34% | NA |
| Indica II | 465 | 84.10% | 15.30% | 0.22% | 0.43% | NA |
| Indica III | 913 | 20.20% | 75.20% | 0.66% | 3.94% | NA |
| Indica Intermediate | 786 | 35.10% | 63.10% | 0.00% | 1.78% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 26.70% | 0.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424199521 | G -> DEL | N | N | silent_mutation | Average:35.438; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199521 | G -> GCA | LOC_Os04g40770.1 | downstream_gene_variant ; 4172.0bp to feature; MODIFIER | silent_mutation | Average:35.438; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199521 | G -> GCA | LOC_Os04g40790.1 | downstream_gene_variant ; 2791.0bp to feature; MODIFIER | silent_mutation | Average:35.438; most accessible tissue: Callus, score: 76.576 | N | N | N | N |
| vg0424199521 | G -> GCA | LOC_Os04g40780.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.438; most accessible tissue: Callus, score: 76.576 | N | N | N | N |