| Variant ID: vg0609017853 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017853 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTATTCGAATAGCCGCGCCCTCGGTTATGGGCAAGCCGAGCAATGTACCCAAGTTAGTGTTTTAATTCTTAAAACCTGCTTAACGACTAAAATGTGGAA[T/A]
GGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGG
CCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACC[A/T]
TTCCACATTTTAGTCGTTAAGCAGGTTTTAAGAATTAAAACACTAACTTGGGTACATTGCTCGGCTTGCCCATAACCGAGGGCGCGGCTATTCGAATAGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.90% | 0.10% | 10.50% | 38.47% | NA |
| All Indica | 2759 | 60.00% | 0.20% | 8.37% | 31.46% | NA |
| All Japonica | 1512 | 41.00% | 0.00% | 11.77% | 47.22% | NA |
| Aus | 269 | 28.60% | 0.70% | 14.50% | 56.13% | NA |
| Indica I | 595 | 57.60% | 0.00% | 2.86% | 39.50% | NA |
| Indica II | 465 | 79.40% | 0.00% | 7.31% | 13.33% | NA |
| Indica III | 913 | 46.10% | 0.20% | 13.25% | 40.42% | NA |
| Indica Intermediate | 786 | 66.40% | 0.40% | 7.51% | 25.70% | NA |
| Temperate Japonica | 767 | 73.40% | 0.00% | 1.83% | 24.77% | NA |
| Tropical Japonica | 504 | 5.40% | 0.00% | 22.22% | 72.42% | NA |
| Japonica Intermediate | 241 | 12.40% | 0.00% | 21.58% | 65.98% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 35.42% | 57.29% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 15.56% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017853 | T -> A | LOC_Os06g15870.1 | upstream_gene_variant ; 3238.0bp to feature; MODIFIER | silent_mutation | Average:30.025; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 | N | N | N | N |
| vg0609017853 | T -> A | LOC_Os06g15900.1 | upstream_gene_variant ; 3561.0bp to feature; MODIFIER | silent_mutation | Average:30.025; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 | N | N | N | N |
| vg0609017853 | T -> A | LOC_Os06g15890.1 | downstream_gene_variant ; 1495.0bp to feature; MODIFIER | silent_mutation | Average:30.025; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 | N | N | N | N |
| vg0609017853 | T -> A | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.025; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 | N | N | N | N |
| vg0609017853 | T -> DEL | N | N | silent_mutation | Average:30.025; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 | N | N | N | N |