| Variant ID: vg0334133715 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34133715 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 386. )
ACCTAAGACCACTGGTAGAAGATCTTAAACAGTTGTGGAAGAAGGAAGGTGTCCCCGTGTGGGACGAGGACAAACAGGAGGAGTTTAACCTACGAGCGCT[G/A]
CTGTTCGTAACCATCAACGATTGGCCTGCACTTAGCAACCTATCCGGACAGTCCAACAAGGGGTACAAGGCTTGCACTCACTGTATGGATGAAACAGAAA
TTTCTGTTTCATCCATACAGTGAGTGCAAGCCTTGTACCCCTTGTTGGACTGTCCGGATAGGTTGCTAAGTGCAGGCCAATCGTTGATGGTTACGAACAG[C/T]
AGCGCTCGTAGGTTAAACTCCTCCTGTTTGTCCTCGTCCCACACGGGGACACCTTCCTTCTTCCACAACTGTTTAAGATCTTCTACCAGTGGTCTTAGGT
| 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 | 19.00% | 0.10% | 15.13% | 65.74% | NA |
| All Indica | 2759 | 30.60% | 0.10% | 16.96% | 52.41% | NA |
| All Japonica | 1512 | 0.70% | 0.10% | 13.89% | 85.32% | NA |
| Aus | 269 | 11.50% | 0.00% | 6.32% | 82.16% | NA |
| Indica I | 595 | 9.60% | 0.00% | 7.56% | 82.86% | NA |
| Indica II | 465 | 34.40% | 0.00% | 15.48% | 50.11% | NA |
| Indica III | 913 | 43.80% | 0.20% | 20.15% | 35.82% | NA |
| Indica Intermediate | 786 | 28.80% | 0.00% | 21.25% | 50.00% | NA |
| Temperate Japonica | 767 | 0.70% | 0.00% | 4.30% | 95.05% | NA |
| Tropical Japonica | 504 | 0.40% | 0.40% | 29.17% | 70.04% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 12.45% | 86.31% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 5.21% | 91.67% | NA |
| Intermediate | 90 | 14.40% | 0.00% | 16.67% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334133715 | G -> A | LOC_Os03g60010.1 | synonymous_variant ; p.Leu428Leu; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0334133715 | G -> DEL | LOC_Os03g60010.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |