| Variant ID: vg0137237029 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 37237029 |
| Reference Allele: T | Alternative Allele: TGAAAC,G |
| Primary Allele: T | Secondary Allele: TGAAAC |
Inferred Ancestral Allele: Not determined.
TTATAATACTTCCTCCGTTCCATAATGTACATTATGTTATTCTAGCATTTTCTATATCCATATAATATAGATGTGGAAAATGATAGAATGACTTACATTA[T/TGAAAC,G]
GAAACGGATATTTGAGTATATATGTAGCACAGTGATGTGTAGGAGCATGTGTTGATTGCTTTCGGTTACCGGTCAGACGTTTAGACCGTAGCTTACCATT
AATGGTAAGCTACGGTCTAAACGTCTGACCGGTAACCGAAAGCAATCAACACATGCTCCTACACATCACTGTGCTACATATATACTCAAATATCCGTTTC[A/GTTTCA,C]
TAATGTAAGTCATTCTATCATTTTCCACATCTATATTATATGGATATAGAAAATGCTAGAATAACATAATGTACATTATGGAACGGAGGAAGTATTATAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TGAAAC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.60% | 1.10% | 0.30% | 0.00% | G: 0.04% |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.80% | 3.20% | 0.93% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.40% | 0.50% | 1.04% | 0.00% | NA |
| Tropical Japonica | 504 | 96.60% | 3.00% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.90% | 12.40% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 0.00% | 0.00% | G: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137237029 | T -> G | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 204.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237029 | T -> G | LOC_Os01g64110.1 | upstream_gene_variant ; 1872.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237029 | T -> G | LOC_Os01g64120.1 | upstream_gene_variant ; 4126.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237029 | T -> G | LOC_Os01g64090.1 | downstream_gene_variant ; 2654.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237029 | T -> TGAAAC | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 211.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237029 | T -> TGAAAC | LOC_Os01g64110.1 | upstream_gene_variant ; 1871.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237029 | T -> TGAAAC | LOC_Os01g64120.1 | upstream_gene_variant ; 4125.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237029 | T -> TGAAAC | LOC_Os01g64090.1 | downstream_gene_variant ; 2655.0bp to feature; MODIFIER | silent_mutation | Average:74.82; most accessible tissue: Callus, score: 91.532 | N | N | N | N |