| Variant ID: vg1101693431 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 1693431 |
| Reference Allele: T | Alternative Allele: TC |
| Primary Allele: T | Secondary Allele: TC |
Inferred Ancestral Allele: Not determined.
GAGCTCAAAAATGGGTTAGCAAAGCAGGGCACCAAGTTTTCAGACAACGAAATTGAGCAACTGATGGAAGCAGTGAGTCCTCATAGTGAAGCTACAAACT[T/TC]
AGTTCAGTTCGAGATGAAATGCTAAAACTGACAGGACTCCTGGAAATTCCTTTCAACTTTCAGGCTGATGCTGATGGCAATGGAATTATCGACTATGAGG
CCTCATAGTCGATAATTCCATTGCCATCAGCATCAGCCTGAAAGTTGAAAGGAATTTCCAGGAGTCCTGTCAGTTTTAGCATTTCATCTCGAACTGAACT[A/GA]
AGTTTGTAGCTTCACTATGAGGACTCACTGCTTCCATCAGTTGCTCAATTTCGTTGTCTGAAAACTTGGTGCCCTGCTTTGCTAACCCATTTTTGAGCTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.40% | 0.20% | 13.29% | 24.04% | NA |
| All Indica | 2759 | 41.40% | 0.30% | 19.72% | 38.64% | NA |
| All Japonica | 1512 | 97.90% | 0.00% | 1.65% | 0.40% | NA |
| Aus | 269 | 61.00% | 1.10% | 15.99% | 21.93% | NA |
| Indica I | 595 | 90.10% | 0.00% | 3.87% | 6.05% | NA |
| Indica II | 465 | 32.50% | 0.40% | 27.96% | 39.14% | NA |
| Indica III | 913 | 14.90% | 0.50% | 20.70% | 63.86% | NA |
| Indica Intermediate | 786 | 40.50% | 0.10% | 25.70% | 33.72% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.91% | 0.78% | NA |
| Tropical Japonica | 504 | 96.80% | 0.00% | 3.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 14.44% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101693431 | T -> TC | LOC_Os11g04160.1 | downstream_gene_variant ; 2092.0bp to feature; MODIFIER | silent_mutation | Average:40.693; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1101693431 | T -> TC | LOC_Os11g04174.1 | downstream_gene_variant ; 1040.0bp to feature; MODIFIER | silent_mutation | Average:40.693; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1101693431 | T -> TC | LOC_Os11g04180.1 | downstream_gene_variant ; 2995.0bp to feature; MODIFIER | silent_mutation | Average:40.693; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1101693431 | T -> TC | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:40.693; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1101693431 | T -> DEL | N | N | silent_mutation | Average:40.693; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |