| Variant ID: vg0123775860 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 23775860 |
| Reference Allele: GT | Alternative Allele: GTTT,GTTTT,GTTTTT,GTT,G |
| Primary Allele: GT | Secondary Allele: GTTTT |
Inferred Ancestral Allele: Not determined.
AGCTTGATTTCTACGGCCAGAAGAAGTCATTGTAGAAAAATCTCAATGAGTGAAATAGCTTAGATCGTAAGAATACTCACAAATTAATGCATACCCTAGA[GT/GTTT,GTTTT,GTTTTT,GTT,G]
TTTTTTTTTTGAAATACACAAAAGACTTGCATATCATTGCATTAAGAGGAGTAAAGTAATACAAGACAGACAGAGAAGAACAGGGAGGAGAGAGGAGGGG
CCCCTCCTCTCTCCTCCCTGTTCTTCTCTGTCTGTCTTGTATTACTTTACTCCTCTTAATGCAATGATATGCAAGTCTTTTGTGTATTTCAAAAAAAAAA[AC/AAAC,AAAAC,AAAAAC,AAC,C]
TCTAGGGTATGCATTAATTTGTGAGTATTCTTACGATCTAAGCTATTTCACTCATTGAGATTTTTCTACAATGACTTCTTCTGGCCGTAGAAATCAAGCT
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of GTTTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 21.60% | 7.20% | 4.36% | 56.14% | GTT: 7.02%; GTTT: 2.52%; GTTTTT: 0.61%; G: 0.55% |
| All Indica | 2759 | 2.70% | 4.30% | 2.32% | 89.34% | GTT: 0.62%; GTTT: 0.54%; GTTTTT: 0.14% |
| All Japonica | 1512 | 59.50% | 5.70% | 3.44% | 7.87% | GTT: 20.17%; G: 1.65%; GTTT: 1.65%; GTTTTT: 0.07% |
| Aus | 269 | 4.10% | 47.60% | 23.79% | 13.01% | GTTTTT: 7.06%; GTTT: 4.46% |
| Indica I | 595 | 2.90% | 0.00% | 1.18% | 95.97% | NA |
| Indica II | 465 | 3.00% | 1.90% | 1.51% | 92.69% | GTT: 0.65%; GTTT: 0.22% |
| Indica III | 913 | 0.70% | 6.70% | 2.63% | 88.50% | GTTT: 0.88%; GTT: 0.44%; GTTTTT: 0.22% |
| Indica Intermediate | 786 | 4.70% | 6.40% | 3.31% | 83.33% | GTT: 1.27%; GTTT: 0.76%; GTTTTT: 0.25% |
| Temperate Japonica | 767 | 67.10% | 0.10% | 3.13% | 0.52% | GTT: 26.08%; G: 2.87%; GTTT: 0.13% |
| Tropical Japonica | 504 | 44.00% | 15.50% | 4.37% | 20.83% | GTT: 12.90%; GTTT: 1.98%; GTTTTT: 0.20%; G: 0.20% |
| Japonica Intermediate | 241 | 67.20% | 2.90% | 2.49% | 4.15% | GTT: 16.60%; GTTT: 5.81%; G: 0.83% |
| VI/Aromatic | 96 | 7.30% | 1.00% | 15.62% | 1.04% | GTTT: 67.71%; GTT: 4.17%; GTTTTT: 3.12% |
| Intermediate | 90 | 35.60% | 3.30% | 12.22% | 36.67% | GTT: 6.67%; GTTTTT: 2.22%; GTTT: 2.22%; G: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123775860 | GT -> G | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 631.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> G | LOC_Os01g41920.1 | upstream_gene_variant ; 3178.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> G | LOC_Os01g41910.1 | downstream_gene_variant ; 4346.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTTT | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 630.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTTT | LOC_Os01g41920.1 | upstream_gene_variant ; 3179.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTTT | LOC_Os01g41910.1 | downstream_gene_variant ; 4347.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTT | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 630.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTT | LOC_Os01g41920.1 | upstream_gene_variant ; 3179.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTT | LOC_Os01g41910.1 | downstream_gene_variant ; 4347.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTT | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 630.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTT | LOC_Os01g41920.1 | upstream_gene_variant ; 3179.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTT | LOC_Os01g41910.1 | downstream_gene_variant ; 4347.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTTTT | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 630.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTTTT | LOC_Os01g41920.1 | upstream_gene_variant ; 3179.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> GTTTTT | LOC_Os01g41910.1 | downstream_gene_variant ; 4347.0bp to feature; MODIFIER | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775860 | GT -> DEL | N | N | silent_mutation | Average:10.782; most accessible tissue: Callus, score: 62.341 | N | N | N | N |