| Variant ID: vg0623601535 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23601535 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATTTTTCTCACGAGAGGTGGCAGTGGCGTATTTAGAATTTTTAAATGGATAGTCCAACCTATATATTTTTTTAAAATACCCTAAACATAACCAGGTTAG[T/A]
TGTATAAATTGATCAAATGTGTATCATAATATATTCATAAGGGTTTTTTCTCAAAAGTTTATTTTCATATATGTACATATATGCATTAGGCTAGAATTTT
AAAATTCTAGCCTAATGCATATATGTACATATATGAAAATAAACTTTTGAGAAAAAACCCTTATGAATATATTATGATACACATTTGATCAATTTATACA[A/T]
CTAACCTGGTTATGTTTAGGGTATTTTAAAAAAATATATAGGTTGGACTATCCATTTAAAAATTCTAAATACGCCACTGCCACCTCTCGTGAGAAAAATC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.20% | 4.90% | 3.62% | 1.25% | NA |
| All Indica | 2759 | 92.20% | 0.10% | 5.62% | 2.03% | NA |
| All Japonica | 1512 | 84.40% | 14.70% | 0.79% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.00% | 0.00% | 3.19% | 0.84% | NA |
| Indica II | 465 | 83.70% | 0.40% | 12.69% | 3.23% | NA |
| Indica III | 913 | 96.30% | 0.00% | 1.53% | 2.19% | NA |
| Indica Intermediate | 786 | 89.80% | 0.10% | 8.02% | 2.04% | NA |
| Temperate Japonica | 767 | 71.20% | 27.40% | 1.43% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 95.00% | 4.60% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 5.60% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623601535 | T -> A | LOC_Os06g39756-LOC_Os06g39750 | intergenic_region ; MODIFIER | silent_mutation | Average:54.473; most accessible tissue: Zhenshan97 flower, score: 84.504 | N | N | N | N |
| vg0623601535 | T -> DEL | N | N | silent_mutation | Average:54.473; most accessible tissue: Zhenshan97 flower, score: 84.504 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623601535 | NA | 2.24E-07 | mr1763 | 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 |
| vg0623601535 | NA | 4.57E-06 | mr1910 | 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 |
| vg0623601535 | NA | 1.22E-08 | mr1977 | 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 |
| vg0623601535 | 3.83E-06 | NA | mr1691_2 | 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 |