| Variant ID: vg1007671320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671320 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GACGAGACGCTGGAACTCCGATAGGATCGGCATCGGACATTTAATTGACACAGAACTCAATAGCCTCCTCGGTCGTGTAACCTTCAATGATGCTCCCCTC[G/A]
GGTTTAGCTCTGTTACGAACGTACAACTTCAGAACTCCCATGTACCTTTCAAACGGCCACATTTCCCTTAGAAAAGCCGGGCCACATAGTTTTGTTTGCT
AGCAAACAAAACTATGTGGCCCGGCTTTTCTAAGGGAAATGTGGCCGTTTGAAAGGTACATGGGAGTTCTGAAGTTGTACGTTCGTAACAGAGCTAAACC[C/T]
GAGGGGAGCATCATTGAAGGTTACACGACCGAGGAGGCTATTGAGTTCTGTGTCAATTAAATGTCCGATGCCGATCCTATCGGAGTTCCAGCGTCTCGTC
| 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 | 48.60% | 7.20% | 25.54% | 18.71% | NA |
| All Indica | 2759 | 56.40% | 0.10% | 26.17% | 17.25% | NA |
| All Japonica | 1512 | 36.80% | 21.40% | 17.66% | 24.21% | NA |
| Aus | 269 | 42.80% | 0.00% | 55.39% | 1.86% | NA |
| Indica I | 595 | 34.30% | 0.20% | 46.72% | 18.82% | NA |
| Indica II | 465 | 73.50% | 0.00% | 17.20% | 9.25% | NA |
| Indica III | 913 | 57.00% | 0.10% | 20.04% | 22.89% | NA |
| Indica Intermediate | 786 | 62.50% | 0.30% | 23.03% | 14.25% | NA |
| Temperate Japonica | 767 | 42.10% | 36.80% | 14.34% | 6.78% | NA |
| Tropical Japonica | 504 | 19.80% | 2.60% | 22.82% | 54.76% | NA |
| Japonica Intermediate | 241 | 55.20% | 11.60% | 17.43% | 15.77% | NA |
| VI/Aromatic | 96 | 28.10% | 5.20% | 42.71% | 23.96% | NA |
| Intermediate | 90 | 46.70% | 6.70% | 31.11% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671320 | G -> A | LOC_Os10g14120.1 | upstream_gene_variant ; 3743.0bp to feature; MODIFIER | silent_mutation | Average:7.76; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671320 | G -> A | LOC_Os10g14140.1 | downstream_gene_variant ; 1692.0bp to feature; MODIFIER | silent_mutation | Average:7.76; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671320 | G -> A | LOC_Os10g14150.1 | downstream_gene_variant ; 3955.0bp to feature; MODIFIER | silent_mutation | Average:7.76; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671320 | G -> A | LOC_Os10g14130.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.76; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1007671320 | G -> DEL | N | N | silent_mutation | Average:7.76; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |