| Variant ID: vg0322193677 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22193677 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTTGAGGTTGGGACCTGGGCACGAGCCCTCGTTCAAGCCAAGACACAGAAGGACCGCGGCACAGACCATCCTCGTCTCATACACATAACAAACATAACT[G/A]
ACGTAGAAATTTCCTCTTTATTTGATTACAGATTAAATCAGTCTATACAAGAAGGGGGCCCGAAGGCCTCGGAAGAAGAAGGAGAAGTTATTAAGATTGG
CCAATCTTAATAACTTCTCCTTCTTCTTCCGAGGCCTTCGGGCCCCCTTCTTGTATAGACTGATTTAATCTGTAATCAAATAAAGAGGAAATTTCTACGT[C/T]
AGTTATGTTTGTTATGTGTATGAGACGAGGATGGTCTGTGCCGCGGTCCTTCTGTGTCTTGGCTTGAACGAGGGCTCGTGCCCAGGTCCCAACCTCAAGC
| 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 | 62.10% | 0.40% | 1.38% | 36.14% | NA |
| All Indica | 2759 | 47.40% | 0.70% | 1.27% | 50.60% | NA |
| All Japonica | 1512 | 93.10% | 0.00% | 0.26% | 6.68% | NA |
| Aus | 269 | 48.70% | 0.00% | 8.92% | 42.38% | NA |
| Indica I | 595 | 25.70% | 0.00% | 0.67% | 73.61% | NA |
| Indica II | 465 | 33.30% | 1.10% | 2.80% | 62.80% | NA |
| Indica III | 913 | 73.80% | 0.50% | 1.20% | 24.42% | NA |
| Indica Intermediate | 786 | 41.60% | 1.10% | 0.89% | 56.36% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 94.60% | 0.00% | 0.60% | 4.76% | NA |
| Japonica Intermediate | 241 | 72.20% | 0.00% | 0.00% | 27.80% | NA |
| VI/Aromatic | 96 | 29.20% | 0.00% | 1.04% | 69.79% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 1.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322193677 | G -> A | LOC_Os03g39930.1 | splice_region_variant ; LOW | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193677 | G -> A | LOC_Os03g39930.1 | 3_prime_UTR_variant ; 116.0bp to feature; MODIFIER | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193677 | G -> A | LOC_Os03g39920.1 | downstream_gene_variant ; 507.0bp to feature; MODIFIER | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193677 | G -> A | LOC_Os03g39940.1 | downstream_gene_variant ; 4218.0bp to feature; MODIFIER | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193677 | G -> DEL | N | N | silent_mutation | Average:12.585; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |