| Variant ID: vg1220235240 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20235240 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GACAAGCCTACTATATGCTAGCCGACCGGGAGTATGCTCACACGCGAGAATACTCACCGGAGCTGATAAAAAAGATAGGTATGGATACTGAATTTCGTGC[T/A]
ATTTGGAAAGCTGTTGGTTGGCAGAAATTTGCTATGGTAGATGAGCCTGGTTCTCGTTTGCTTACTTTGCAATTTCTGTGCACTTTGAAAGAAATAGAAG
CTTCTATTTCTTTCAAAGTGCACAGAAATTGCAAAGTAAGCAAACGAGAACCAGGCTCATCTACCATAGCAAATTTCTGCCAACCAACAGCTTTCCAAAT[A/T]
GCACGAAATTCAGTATCCATACCTATCTTTTTTATCAGCTCCGGTGAGTATTCTCGCGTGTGAGCATACTCCCGGTCGGCTAGCATATAGTAGGCTTGTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.30% | 1.50% | 1.93% | 24.35% | NA |
| All Indica | 2759 | 71.00% | 1.70% | 2.17% | 25.15% | NA |
| All Japonica | 1512 | 82.80% | 0.70% | 0.20% | 16.34% | NA |
| Aus | 269 | 40.50% | 3.70% | 10.04% | 45.72% | NA |
| Indica I | 595 | 77.10% | 2.00% | 2.69% | 18.15% | NA |
| Indica II | 465 | 71.80% | 0.20% | 1.08% | 26.88% | NA |
| Indica III | 913 | 66.90% | 1.90% | 2.41% | 28.81% | NA |
| Indica Intermediate | 786 | 70.50% | 2.20% | 2.16% | 25.19% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.00% | 4.04% | NA |
| Tropical Japonica | 504 | 66.10% | 1.40% | 0.60% | 31.94% | NA |
| Japonica Intermediate | 241 | 75.90% | 1.20% | 0.00% | 22.82% | NA |
| VI/Aromatic | 96 | 30.20% | 0.00% | 1.04% | 68.75% | NA |
| Intermediate | 90 | 74.40% | 2.20% | 0.00% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220235240 | T -> DEL | LOC_Os12g33500.1 | N | frameshift_variant | Average:11.334; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1220235240 | T -> A | LOC_Os12g33500.1 | synonymous_variant ; p.Ala88Ala; LOW | synonymous_codon | Average:11.334; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1220235240 | 3.53E-06 | 3.53E-06 | mr1323 | 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 |
| vg1220235240 | 1.76E-06 | 1.76E-06 | mr1421 | 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 |