| Variant ID: vg0609018001 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9018001 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGACCTTGATAAATAATATTGTTTAGTTTTAGAATCGCGTTTA[C/T]
AAAATGGCTTTGAGCAACTAATGTCTTTAAATGCTGTTTACTGCAATCCTAACCCTTTATAGTGTAACTCCTTTGTACTCCCTTGCATTTATTCTGCACT
AGTGCAGAATAAATGCAAGGGAGTACAAAGGAGTTACACTATAAAGGGTTAGGATTGCAGTAAACAGCATTTAAAGACATTAGTTGCTCAAAGCCATTTT[G/A]
TAAACGCGATTCTAAAACTAAACAATATTATTTATCAAGGTCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.90% | 0.00% | 8.51% | 40.52% | NA |
| All Indica | 2759 | 59.30% | 0.10% | 6.85% | 33.78% | NA |
| All Japonica | 1512 | 42.30% | 0.00% | 9.33% | 48.35% | NA |
| Aus | 269 | 27.10% | 0.00% | 10.04% | 62.83% | NA |
| Indica I | 595 | 57.10% | 0.00% | 2.35% | 40.50% | NA |
| Indica II | 465 | 78.70% | 0.00% | 7.74% | 13.55% | NA |
| Indica III | 913 | 45.30% | 0.20% | 9.75% | 44.69% | NA |
| Indica Intermediate | 786 | 65.60% | 0.00% | 6.36% | 27.99% | NA |
| Temperate Japonica | 767 | 73.90% | 0.00% | 1.56% | 24.51% | NA |
| Tropical Japonica | 504 | 7.50% | 0.00% | 17.26% | 75.20% | NA |
| Japonica Intermediate | 241 | 14.50% | 0.00% | 17.43% | 68.05% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 34.38% | 55.21% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 13.33% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609018001 | C -> T | LOC_Os06g15870.1 | upstream_gene_variant ; 3386.0bp to feature; MODIFIER | silent_mutation | Average:29.949; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0609018001 | C -> T | LOC_Os06g15900.1 | upstream_gene_variant ; 3413.0bp to feature; MODIFIER | silent_mutation | Average:29.949; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0609018001 | C -> T | LOC_Os06g15890.1 | downstream_gene_variant ; 1347.0bp to feature; MODIFIER | silent_mutation | Average:29.949; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0609018001 | C -> T | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:29.949; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0609018001 | C -> DEL | N | N | silent_mutation | Average:29.949; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |