| Variant ID: vg0208339463 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8339463 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTTTATTATATGCATATCTTTAAGGGGAGCTTCATACTTCTCTCATCATTCCAAATTTAAATTCTATTATCTTTTTGTGTGCTTTAACCATGTTGTCAT[C/T]
AATCACCAAAAAGGGGGAGATTGAAGATGCACTTAAACCCCTAGTGGGTTTTGGTGATTAATGACAAGGTGGTTAAAGGGGACTAACGTGTTTATCAAGT
ACTTGATAAACACGTTAGTCCCCTTTAACCACCTTGTCATTAATCACCAAAACCCACTAGGGGTTTAAGTGCATCTTCAATCTCCCCCTTTTTGGTGATT[G/A]
ATGACAACATGGTTAAAGCACACAAAAAGATAATAGAATTTAAATTTGGAATGATGAGAGAAGTATGAAGCTCCCCTTAAAGATATGCATATAATAAAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 1.90% | 4.25% | 2.86% | NA |
| All Indica | 2759 | 96.70% | 1.00% | 2.21% | 0.11% | NA |
| All Japonica | 1512 | 79.10% | 4.00% | 8.33% | 8.60% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.60% | 3.40% | 4.03% | 0.00% | NA |
| Indica II | 465 | 98.70% | 0.20% | 1.08% | 0.00% | NA |
| Indica III | 913 | 97.40% | 0.20% | 2.30% | 0.11% | NA |
| Indica Intermediate | 786 | 97.70% | 0.60% | 1.40% | 0.25% | NA |
| Temperate Japonica | 767 | 84.10% | 0.40% | 2.22% | 13.30% | NA |
| Tropical Japonica | 504 | 70.20% | 10.10% | 16.67% | 2.98% | NA |
| Japonica Intermediate | 241 | 81.70% | 2.50% | 10.37% | 5.39% | NA |
| VI/Aromatic | 96 | 85.40% | 1.00% | 12.50% | 1.04% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208339463 | C -> T | LOC_Os02g14929.1 | intron_variant ; MODIFIER | silent_mutation | Average:18.899; most accessible tissue: Minghui63 flag leaf, score: 30.782 | N | N | N | N |
| vg0208339463 | C -> DEL | N | N | silent_mutation | Average:18.899; most accessible tissue: Minghui63 flag leaf, score: 30.782 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0208339463 | 4.55E-06 | 4.67E-06 | mr1415 | 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 |
| vg0208339463 | 4.55E-06 | 4.67E-06 | mr1567 | 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 |