| Variant ID: vg0139513400 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39513400 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 331. )
CTAATCTCTTCCAAAGCTCATTGAATTTTTTCTCCTGGTTCTGATTGCACAGCCTCTTGAACATGTTCATGAGCTCCTTGTTCTTGAATTGCTTGAAGAA[A/G]
TTAGCTCCCATATGACGCATGCACCACCTACTCTGTACATCTTCCCAAACACCGGGGTATCCTCGTTCCATACTCCCAAACTGCAACTCTCCTATCGCTC
GAGCGATAGGAGAGTTGCAGTTTGGGAGTATGGAACGAGGATACCCCGGTGTTTGGGAAGATGTACAGAGTAGGTGGTGCATGCGTCATATGGGAGCTAA[T/C]
TTCTTCAAGCAATTCAAGAACAAGGAGCTCATGAACATGTTCAAGAGGCTGTGCAATCAGAACCAGGAGAAAAAATTCAATGAGCTTTGGAAGAGATTAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 8.90% | 0.30% | 13.37% | 77.42% | NA |
| All Indica | 2759 | 0.30% | 0.00% | 1.78% | 97.90% | NA |
| All Japonica | 1512 | 25.90% | 0.90% | 35.65% | 37.50% | NA |
| Aus | 269 | 0.00% | 0.00% | 2.23% | 97.77% | NA |
| Indica I | 595 | 0.50% | 0.00% | 1.34% | 98.15% | NA |
| Indica II | 465 | 0.60% | 0.00% | 0.43% | 98.92% | NA |
| Indica III | 913 | 0.10% | 0.00% | 1.42% | 98.47% | NA |
| Indica Intermediate | 786 | 0.30% | 0.00% | 3.31% | 96.44% | NA |
| Temperate Japonica | 767 | 22.30% | 0.30% | 47.59% | 29.86% | NA |
| Tropical Japonica | 504 | 36.90% | 2.00% | 23.21% | 37.90% | NA |
| Japonica Intermediate | 241 | 14.50% | 0.80% | 23.65% | 61.00% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 22.92% | 75.00% | NA |
| Intermediate | 90 | 18.90% | 1.10% | 17.78% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139513400 | A -> G | LOC_Os01g67990.1 | synonymous_variant ; p.Asn498Asn; LOW | synonymous_codon | Average:6.529; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0139513400 | A -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:6.529; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |