| Variant ID: vg0324101632 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 24101632 |
| Reference Allele: G | Alternative Allele: A,C,GT |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 32. )
AAGCAACATCAACCATCTGATCGGCTACTGGCATTGGATACTCATCCTTTGGGGTAGCTTTGTTTAAATCCCTGAAATCAATACACACCTTGACTTTGCC[G/A,C,GT]
TTTTTCTTGATAACTGGAACTATACTAGAAACCCACTCGGCATATCGACAAGGACGAATAAAATCAGCATCATATAAACGTTTAATCTTAGCCTTGACAG
CTGTCAAGGCTAAGATTAAACGTTTATATGATGCTGATTTTATTCGTCCTTGTCGATATGCCGAGTGGGTTTCTAGTATAGTTCCAGTTATCAAGAAAAA[C/T,G,AC]
GGCAAAGTCAAGGTGTGTATTGATTTCAGGGATTTAAACAAAGCTACCCCAAAGGATGAGTATCCAATGCCAGTAGCCGATCAGATGGTTGATGTTGCTT
| 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 | 71.90% | 3.30% | 18.39% | 6.47% | NA |
| All Indica | 2759 | 53.00% | 5.30% | 30.88% | 10.76% | NA |
| All Japonica | 1512 | 99.10% | 0.10% | 0.20% | 0.53% | NA |
| Aus | 269 | 97.00% | 1.10% | 1.49% | 0.37% | NA |
| Indica I | 595 | 59.30% | 5.40% | 27.23% | 8.07% | NA |
| Indica II | 465 | 61.70% | 4.10% | 25.59% | 8.60% | NA |
| Indica III | 913 | 43.30% | 5.50% | 35.82% | 15.44% | NA |
| Indica Intermediate | 786 | 54.50% | 5.90% | 31.04% | 8.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 0.20% | 0.60% | 1.59% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 2.20% | 11.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324101632 | G -> C | LOC_Os03g43220.1 | missense_variant ; p.Asn1092Lys; MODERATE | N | Average:16.085; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0324101632 | G -> C | LOC_Os03g43230.1 | upstream_gene_variant ; 4393.0bp to feature; MODIFIER | N | Average:16.085; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0324101632 | G -> C | LOC_Os03g43210.1 | downstream_gene_variant ; 3192.0bp to feature; MODIFIER | N | Average:16.085; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0324101632 | G -> GT | LOC_Os03g43220.1 | frameshift_variant ; p.Asn1092fs; HIGH | N | Average:16.085; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0324101632 | G -> GT | LOC_Os03g43230.1 | upstream_gene_variant ; 4392.0bp to feature; MODIFIER | N | Average:16.085; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0324101632 | G -> A | LOC_Os03g43220.1 | synonymous_variant ; p.Asn1092Asn; LOW | synonymous_codon | Average:16.085; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0324101632 | G -> DEL | LOC_Os03g43220.1 | N | frameshift_variant | Average:16.085; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0324101632 | NA | 5.82E-15 | mr1916 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0324101632 | 3.52E-06 | NA | mr1539_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0324101632 | NA | 2.00E-06 | mr1559_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |