| Variant ID: vg0503844373 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 3844373 |
| Reference Allele: TA | Alternative Allele: AA,T |
| Primary Allele: TA | Secondary Allele: AA |
Inferred Ancestral Allele: Not determined.
GGAGGGCCAACTAGTTAATTAATGTGTTTCACCATCACATTATAGATTTCATAAGAGATGTACTAGGATTGTGGGAGTACTTCTCAATTTCGTTTTTTTT[TA/AA,T]
AAAAAAATGCACTTTTGAACATTAACTGTTGTCTTGAGCATAAACATGCAAAATGTGTATAACCAAGAATATATGATCTTCCTAGTAATGGTGCTCAAAA
TTTTGAGCACCATTACTAGGAAGATCATATATTCTTGGTTATACACATTTTGCATGTTTATGCTCAAGACAACAGTTAATGTTCAAAAGTGCATTTTTTT[TA/TT,A]
AAAAAAAACGAAATTGAGAAGTACTCCCACAATCCTAGTACATCTCTTATGAAATCTATAATGTGATGGTGAAACACATTAATTAACTAGTTGGCCCTCC
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of AA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.10% | 0.40% | 21.43% | 11.07% | T: 0.06% |
| All Indica | 2759 | 57.30% | 0.10% | 32.08% | 10.51% | NA |
| All Japonica | 1512 | 92.90% | 0.80% | 5.62% | 0.46% | T: 0.20% |
| Aus | 269 | 13.00% | 0.00% | 7.06% | 79.93% | NA |
| Indica I | 595 | 44.70% | 0.00% | 46.72% | 8.57% | NA |
| Indica II | 465 | 61.10% | 0.00% | 28.39% | 10.54% | NA |
| Indica III | 913 | 64.10% | 0.30% | 24.42% | 11.17% | NA |
| Indica Intermediate | 786 | 56.60% | 0.10% | 32.06% | 11.20% | NA |
| Temperate Japonica | 767 | 95.60% | 0.70% | 3.65% | 0.13% | NA |
| Tropical Japonica | 504 | 95.80% | 0.40% | 2.98% | 0.20% | T: 0.60% |
| Japonica Intermediate | 241 | 78.40% | 2.10% | 17.43% | 2.07% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 15.62% | 5.21% | NA |
| Intermediate | 90 | 82.20% | 1.10% | 10.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844373 | TA -> T | LOC_Os05g07260.1 | downstream_gene_variant ; 1205.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> T | LOC_Os05g07260.2 | downstream_gene_variant ; 1216.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> T | LOC_Os05g07260.4 | downstream_gene_variant ; 1216.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> T | LOC_Os05g07260.3 | downstream_gene_variant ; 1205.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> T | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> DEL | N | N | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> AA | LOC_Os05g07260.1 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> AA | LOC_Os05g07260.2 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> AA | LOC_Os05g07260.4 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> AA | LOC_Os05g07260.3 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844373 | TA -> AA | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.371; most accessible tissue: Callus, score: 68.266 | N | N | N | N |