| Variant ID: vg1101693429 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 1693429 |
| Reference Allele: CTTAG | Alternative Allele: C |
| Primary Allele: CTTAG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGGAGCTCAAAAATGGGTTAGCAAAGCAGGGCACCAAGTTTTCAGACAACGAAATTGAGCAACTGATGGAAGCAGTGAGTCCTCATAGTGAAGCTACAAA[CTTAG/C]
TTCAGTTCGAGATGAAATGCTAAAACTGACAGGACTCCTGGAAATTCCTTTCAACTTTCAGGCTGATGCTGATGGCAATGGAATTATCGACTATGAGGAG
CTCCTCATAGTCGATAATTCCATTGCCATCAGCATCAGCCTGAAAGTTGAAAGGAATTTCCAGGAGTCCTGTCAGTTTTAGCATTTCATCTCGAACTGAA[CTAAG/G]
TTTGTAGCTTCACTATGAGGACTCACTGCTTCCATCAGTTGCTCAATTTCGTTGTCTGAAAACTTGGTGCCCTGCTTTGCTAACCCATTTTTGAGCTCCT
| Populations | Population Size | Frequency of CTTAG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.10% | 2.70% | 12.65% | 28.61% | NA |
| All Indica | 2759 | 31.60% | 4.20% | 18.74% | 45.38% | NA |
| All Japonica | 1512 | 97.60% | 0.10% | 1.06% | 1.26% | NA |
| Aus | 269 | 54.60% | 1.90% | 17.10% | 26.39% | NA |
| Indica I | 595 | 86.40% | 0.30% | 5.21% | 8.07% | NA |
| Indica II | 465 | 14.20% | 5.20% | 30.75% | 49.89% | NA |
| Indica III | 913 | 5.70% | 6.90% | 17.42% | 69.99% | NA |
| Indica Intermediate | 786 | 30.70% | 3.60% | 23.41% | 42.37% | NA |
| Temperate Japonica | 767 | 98.00% | 0.10% | 0.91% | 0.91% | NA |
| Tropical Japonica | 504 | 96.00% | 0.20% | 1.39% | 2.38% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 68.90% | 3.30% | 18.89% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101693429 | CTTAG -> DEL | N | N | silent_mutation | Average:39.108; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1101693429 | CTTAG -> C | LOC_Os11g04160.1 | downstream_gene_variant ; 2090.0bp to feature; MODIFIER | silent_mutation | Average:39.108; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1101693429 | CTTAG -> C | LOC_Os11g04174.1 | downstream_gene_variant ; 1042.0bp to feature; MODIFIER | silent_mutation | Average:39.108; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1101693429 | CTTAG -> C | LOC_Os11g04180.1 | downstream_gene_variant ; 2997.0bp to feature; MODIFIER | silent_mutation | Average:39.108; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg1101693429 | CTTAG -> C | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.108; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |