| Variant ID: vg1127723835 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 27723835 |
| Reference Allele: T | Alternative Allele: TGG,G,TGGG,TGC |
| Primary Allele: T | Secondary Allele: TGGG |
Inferred Ancestral Allele: Not determined.
TTTGATGTGATAGAAAAATTAAAAGTTCGAAGAAAAAGTTTGTAACTAAACTTGGCCTAGGTTGTTTTTTTTGGATGGCGTAGGTTGTTTTTTTTTTTTT[T/TGG,G,TGGG,TGC]
ATGGAGGGAGTACGTCACATTAAAGTGCCCAACAGCTGCTCAAATGTCCCCGTCGTCTATTCTGAACAGAACTTGTGGAATGGGTGGATGGGCATAAAGA
TCTTTATGCCCATCCACCCATTCCACAAGTTCTGTTCAGAATAGACGACGGGGACATTTGAGCAGCTGTTGGGCACTTTAATGTGACGTACTCCCTCCAT[A/CCA,C,CCCA,GCA]
AAAAAAAAAAAAACAACCTACGCCATCCAAAAAAAACAACCTAGGCCAAGTTTAGTTACAAACTTTTTCTTCGAACTTTTAATTTTTCTATCACATCAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TGGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.20% | 4.80% | 0.49% | 28.04% | G: 1.42%; TGC: 0.87%; TGG: 0.17% |
| All Indica | 2759 | 61.30% | 7.30% | 0.51% | 27.04% | G: 2.36%; TGC: 1.20%; TGG: 0.29% |
| All Japonica | 1512 | 77.70% | 0.90% | 0.33% | 20.50% | TGC: 0.53%; G: 0.07% |
| Aus | 269 | 29.00% | 0.00% | 0.74% | 70.26% | NA |
| Indica I | 595 | 40.80% | 18.30% | 0.67% | 37.98% | G: 2.02%; TGC: 0.17% |
| Indica II | 465 | 46.00% | 12.90% | 1.08% | 32.69% | G: 5.38%; TGC: 1.94% |
| Indica III | 913 | 84.40% | 0.00% | 0.22% | 13.47% | TGC: 1.10%; G: 0.44%; TGG: 0.33% |
| Indica Intermediate | 786 | 58.90% | 4.20% | 0.38% | 31.17% | G: 3.05%; TGC: 1.65%; TGG: 0.64% |
| Temperate Japonica | 767 | 80.60% | 1.40% | 0.13% | 17.60% | TGC: 0.26% |
| Tropical Japonica | 504 | 69.80% | 0.00% | 0.79% | 27.98% | TGC: 1.19%; G: 0.20% |
| Japonica Intermediate | 241 | 85.10% | 0.80% | 0.00% | 14.11% | NA |
| VI/Aromatic | 96 | 33.30% | 0.00% | 1.04% | 64.58% | G: 1.04% |
| Intermediate | 90 | 65.60% | 13.30% | 1.11% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1127723835 | T -> TGG | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 408.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> TGG | LOC_Os11g45809.1 | downstream_gene_variant ; 2736.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> DEL | N | N | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> TGGG | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 408.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> TGGG | LOC_Os11g45809.1 | downstream_gene_variant ; 2736.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> TGC | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 408.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> TGC | LOC_Os11g45809.1 | downstream_gene_variant ; 2736.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> G | LOC_Os11g45820.1 | upstream_gene_variant ; 1.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> G | LOC_Os11g45809.1 | downstream_gene_variant ; 2735.0bp to feature; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
| vg1127723835 | T -> G | LOC_Os11g45809-LOC_Os11g45820 | intergenic_region ; MODIFIER | silent_mutation | Average:39.027; most accessible tissue: Callus, score: 90.438 | N | N | N | N |
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