| Variant ID: vg0420968005 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 20968005 |
| Reference Allele: G | Alternative Allele: GTGTAA,GTGTAACAC,GTGTAACACCCTGAAAATTCAACCAGCGAAAA,GTGTAACACCCTGAAAATTCAACCAGCGAAAACAAAACTCTAAAAATACGGGCTTT |
| Primary Allele: G | Secondary Allele: GTGTAACACCCTGAAAATTC AACCAGCGAAAA |
Inferred Ancestral Allele: Not determined.
ACTTATCTGCGCTCCTACATTTGGAAGGGCTATGGGGAACTTGAGACATAATTTCACCAGAAAAAGTGCTTTCCATGGTTTTAGATAATATGCCAGGCTA[G/GTGTAA,GTGTAACAC,GTGTAACACCCTGAAAATTCAACCAGCGAAAA,GTGTAACACCCTGAAAATTCAACCAGCGAAAACAAAACTCTAAAAATACGGGCTTT]
CAAAATGCTCCATCGATTCTATGCGATCTCTCTTCAAGAAAGAAGTTATGATTGAAAATTCATAACATTGATATATATCTGCACTTTTGTAGTTTGAAGA
TCTTCAAACTACAAAAGTGCAGATATATATCAATGTTATGAATTTTCAATCATAACTTCTTTCTTGAAGAGAGATCGCATAGAATCGATGGAGCATTTTG[C/TTACAC,GTGTTACAC,TTTTCGCTGGTTGAATTTTCAGGGTGTTACAC,AAAGCCCGTATTTTTAGAGTTTTGTTTTCGCTGGTTGAATTTTCAGGGTGTTACAC]
TAGCCTGGCATATTATCTAAAACCATGGAAAGCACTTTTTCTGGTGAAATTATGTCTCAAGTTCCCCATAGCCCTTCCAAATGTAGGAGCGCAGATAAGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GTGTAACACCCTGAAAATTC AACCAGCGAAAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.60% | 0.00% | 0.91% | 1.42% | GTGTAA: 0.02% |
| All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 94.10% | 0.10% | 2.12% | 3.64% | GTGTAA: 0.07% |
| 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 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 85.30% | 0.20% | 5.75% | 8.53% | GTGTAA: 0.20% |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 1.24% | 4.98% | NA |
| VI/Aromatic | 96 | 80.20% | 0.00% | 9.38% | 10.42% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420968005 | G -> DEL | N | N | silent_mutation | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAACACCCTGAAAATTCAACCAGCGAA AACAAAACTCTAAAAATACGGGCTTT | LOC_Os04g34650.1 | upstream_gene_variant ; 3338.0bp to feature; MODIFIER | N | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAACACCCTGAAAATTCAACCAGCGAA AACAAAACTCTAAAAATACGGGCTTT | LOC_Os04g34670.1 | intron_variant ; MODIFIER | N | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAACACCCTGAAAATTCAACCAGCGAA AA | LOC_Os04g34650.1 | upstream_gene_variant ; 3338.0bp to feature; MODIFIER | silent_mutation | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAACACCCTGAAAATTCAACCAGCGAA AA | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAACAC | LOC_Os04g34650.1 | upstream_gene_variant ; 3338.0bp to feature; MODIFIER | N | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAACAC | LOC_Os04g34670.1 | intron_variant ; MODIFIER | N | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAA | LOC_Os04g34650.1 | upstream_gene_variant ; 3338.0bp to feature; MODIFIER | silent_mutation | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0420968005 | G -> GTGTAA | LOC_Os04g34670.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.923; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |