| Variant ID: vg0508328858 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 8328858 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCCAACCGCTACTGGGTTCGCCTTGTTCTTTAGGACGAAATGACCAGGCATCAGCTCCGTGGGTCGAACTTTTTTGTTGTAAGTTGCCGAAGTGCTTGT[G/T]
GCATACTTGTGCATGTGCTCAAGCGCCTCGACTCTTACTCCTTTCAAGAGTTCGAGCGATACTTCGCGTCCTTCTTCGCCCCCAGAGAACATCACCCTTG
CAAGGGTGATGTTCTCTGGGGGCGAAGAAGGACGCGAAGTATCGCTCGAACTCTTGAAAGGAGTAAGAGTCGAGGCGCTTGAGCACATGCACAAGTATGC[C/A]
ACAAGCACTTCGGCAACTTACAACAAAAAAGTTCGACCCACGGAGCTGATGCCTGGTCATTTCGTCCTAAAGAACAAGGCGAACCCAGTAGCGGTTGGCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 70.80% | 27.20% | 1.57% | 0.51% | NA |
| All Indica | 2759 | 53.90% | 43.50% | 2.28% | 0.29% | NA |
| All Japonica | 1512 | 99.20% | 0.50% | 0.26% | 0.00% | NA |
| Aus | 269 | 71.70% | 20.40% | 1.86% | 5.95% | NA |
| Indica I | 595 | 45.50% | 51.10% | 3.36% | 0.00% | NA |
| Indica II | 465 | 57.80% | 40.90% | 1.08% | 0.22% | NA |
| Indica III | 913 | 59.80% | 38.00% | 1.64% | 0.55% | NA |
| Indica Intermediate | 786 | 51.00% | 45.80% | 2.93% | 0.25% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 0.80% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 20.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0508328858 | G -> T | LOC_Os05g14620.1 | synonymous_variant ; p.Ala44Ala; LOW | synonymous_codon | Average:27.378; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| vg0508328858 | G -> DEL | LOC_Os05g14620.1 | N | frameshift_variant | Average:27.378; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0508328858 | 2.34E-06 | 2.97E-06 | mr1115 | 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 |
| vg0508328858 | NA | 1.49E-09 | mr1593 | 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 |
| vg0508328858 | NA | 1.21E-11 | mr1593_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 |