| Variant ID: vg0719562809 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562809 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 368. )
TGGACGTACGCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAGGTGTATACGGAAAGTCGAAAGATACACT[G/A]
GAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTACTTGAGTCCAGCCAGCTACACTC
GAGTGTAGCTGGCTGGACTCAAGTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTC[C/T]
AGTGTATCTTTCGACTTTCCGTATACACCTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGCGTACGTCCA
| 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 | 19.80% | 0.30% | 18.73% | 61.21% | NA |
| All Indica | 2759 | 1.10% | 0.10% | 14.14% | 84.70% | NA |
| All Japonica | 1512 | 59.10% | 0.50% | 24.40% | 15.94% | NA |
| Aus | 269 | 0.00% | 0.00% | 40.52% | 59.48% | NA |
| Indica I | 595 | 0.50% | 0.00% | 3.87% | 95.63% | NA |
| Indica II | 465 | 1.70% | 0.20% | 4.73% | 93.33% | NA |
| Indica III | 913 | 0.40% | 0.10% | 26.07% | 73.38% | NA |
| Indica Intermediate | 786 | 1.90% | 0.00% | 13.61% | 84.48% | NA |
| Temperate Japonica | 767 | 93.00% | 0.10% | 3.00% | 3.91% | NA |
| Tropical Japonica | 504 | 11.30% | 1.00% | 62.90% | 24.80% | NA |
| Japonica Intermediate | 241 | 51.50% | 0.80% | 12.03% | 35.68% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 6.25% | 93.75% | NA |
| Intermediate | 90 | 13.30% | 2.20% | 12.22% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562809 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0719562809 | G -> A | LOC_Os07g32740.1 | synonymous_variant ; p.Leu542Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |