| Variant ID: vg0334748146 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34748146 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CATCCTCATCACTTGAGTAGTCGAAGAGTCTCGGTGGTGATGAAGGCTTGACGGCGAACGTGGCGACTCCTTCTTCATCACTTGAGCTTGACTCGGAGTC[A/G]
GAGCCGTAGATCATCCCAAAGTGAGCTTGGCCATAATGTACCCTCTTGCTATGCTTGTGCTTCTCCTTCTTCTCATCCTTCTTCTCACTCTTCTTCTTAT
ATAAGAAGAAGAGTGAGAAGAAGGATGAGAAGAAGGAGAAGCACAAGCATAGCAAGAGGGTACATTATGGCCAAGCTCACTTTGGGATGATCTACGGCTC[T/C]
GACTCCGAGTCAAGCTCAAGTGATGAAGAAGGAGTCGCCACGTTCGCCGTCAAGCCTTCATCACCACCGAGACTCTTCGACTACTCAAGTGATGAGGATG
| 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 | 60.70% | 39.20% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 92.10% | 7.60% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 2.30% | 97.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 82.90% | 16.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 98.00% | 1.70% | 0.34% | 0.00% | NA |
| Indica II | 465 | 96.10% | 3.70% | 0.22% | 0.00% | NA |
| Indica III | 913 | 87.00% | 12.90% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 91.30% | 8.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 4.80% | 95.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 19.80% | 80.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 54.40% | 45.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334748146 | A -> G | LOC_Os03g61180.1 | synonymous_variant ; p.Ser321Ser; LOW | synonymous_codon | Average:15.794; most accessible tissue: Callus, score: 22.454 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0334748146 | 5.99E-06 | 5.99E-06 | mr1292_2 | Ind_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 |
| vg0334748146 | NA | 2.56E-06 | mr1642_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 |