| Variant ID: vg0609017893 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017893 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCAATGTACCCAAGTTAGTGTTTTAATTCTTAAAACCTGCTTAACGACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGG[G/A]
TCGGGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGGCAGGTTCGTGTGGGTTCACGACCTTGATAAATAATATTGTTTAGTTTTAGAATC
GATTCTAAAACTAAACAATATTATTTATCAAGGTCGTGAACCCACACGAACCTGCCTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACCCGA[C/T]
CCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTCGTTAAGCAGGTTTTAAGAATTAAAACACTAACTTGGGTACATTGC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.00% | 0.40% | 7.79% | 41.77% | NA |
| All Indica | 2759 | 61.40% | 0.10% | 7.03% | 31.53% | NA |
| All Japonica | 1512 | 40.30% | 0.70% | 3.24% | 55.75% | NA |
| Aus | 269 | 5.90% | 2.20% | 39.03% | 52.79% | NA |
| Indica I | 595 | 57.80% | 0.00% | 4.03% | 38.15% | NA |
| Indica II | 465 | 81.30% | 0.00% | 4.95% | 13.76% | NA |
| Indica III | 913 | 48.20% | 0.10% | 10.08% | 41.62% | NA |
| Indica Intermediate | 786 | 67.60% | 0.10% | 7.00% | 25.32% | NA |
| Temperate Japonica | 767 | 72.90% | 0.10% | 0.65% | 26.34% | NA |
| Tropical Japonica | 504 | 5.00% | 1.60% | 6.75% | 86.71% | NA |
| Japonica Intermediate | 241 | 10.80% | 0.40% | 4.15% | 84.65% | NA |
| VI/Aromatic | 96 | 2.10% | 1.00% | 9.38% | 87.50% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 12.22% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017893 | G -> A | LOC_Os06g15870.1 | upstream_gene_variant ; 3278.0bp to feature; MODIFIER | silent_mutation | Average:31.138; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0609017893 | G -> A | LOC_Os06g15900.1 | upstream_gene_variant ; 3521.0bp to feature; MODIFIER | silent_mutation | Average:31.138; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0609017893 | G -> A | LOC_Os06g15890.1 | downstream_gene_variant ; 1455.0bp to feature; MODIFIER | silent_mutation | Average:31.138; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0609017893 | G -> A | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.138; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |
| vg0609017893 | G -> DEL | N | N | silent_mutation | Average:31.138; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 | N | N | N | N |