| Variant ID: vg0825565228 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25565228 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAGGGGTGGTGGCCGGCACTGACGACGGGGTGGCGGTGGCGGTTGGCGATGGCGAAGGAGAGCGCCTTGAGCCAGGTGGTGCCGCACTTTGGGTAGGTGG[C/G]
GAGGAGCACGTCGTCGTCGCGTGGCACGAACTGGGCACGAACCAGCGACACGCTCATCGCTGCCTGCCGGTCCATCCAGCAGCCGTCGTAGAGGACGAAC
GTTCGTCCTCTACGACGGCTGCTGGATGGACCGGCAGGCAGCGATGAGCGTGTCGCTGGTTCGTGCCCAGTTCGTGCCACGCGACGACGACGTGCTCCTC[G/C]
CCACCTACCCAAAGTGCGGCACCACCTGGCTCAAGGCGCTCTCCTTCGCCATCGCCAACCGCCACCGCCACCCCGTCGTCAGTGCCGGCCACCACCCCTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.20% | 9.70% | 1.71% | 16.40% | NA |
| All Indica | 2759 | 71.80% | 0.30% | 1.30% | 26.60% | NA |
| All Japonica | 1512 | 66.50% | 29.00% | 2.78% | 1.72% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 60.00% | 0.30% | 2.86% | 36.81% | NA |
| Indica II | 465 | 46.00% | 0.20% | 1.29% | 52.47% | NA |
| Indica III | 913 | 96.50% | 0.10% | 0.22% | 3.18% | NA |
| Indica Intermediate | 786 | 67.30% | 0.50% | 1.40% | 30.79% | NA |
| Temperate Japonica | 767 | 92.30% | 4.80% | 1.56% | 1.30% | NA |
| Tropical Japonica | 504 | 27.00% | 68.50% | 3.77% | 0.79% | NA |
| Japonica Intermediate | 241 | 66.80% | 23.70% | 4.56% | 4.98% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 13.30% | 3.33% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825565228 | C -> G | LOC_Os08g40380.1 | missense_variant ; p.Ala72Pro; MODERATE | nonsynonymous_codon ; A72P | Average:39.784; most accessible tissue: Zhenshan97 root, score: 85.432 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0825565228 | C -> DEL | LOC_Os08g40380.1 | N | frameshift_variant | Average:39.784; most accessible tissue: Zhenshan97 root, score: 85.432 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0825565228 | NA | 4.71E-06 | mr1364 | Jap_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 |
| vg0825565228 | NA | 5.63E-07 | mr1194_2 | Jap_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 |
| vg0825565228 | 1.26E-06 | 1.31E-07 | mr1715_2 | Jap_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 |