| Variant ID: vg1208919948 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8919948 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 104. )
CGTCTTCCGAATTTCTTCTCCTGGTTTTGAACTTCTATGGTCTTTCTCTTCTCCATTTGAACCCCAATTCTATCGCCTTTCTTAGCATCTTTGCTCATCT[C/T]
TGCGAGGCCTACATTGGGGTAGAGCCTTTTCTTGATCTCTTTCGCTCTTACTACGAACTGCGTTGGATGGAGTCCAACAGGGTATCTGGTTGCGTCGGGT
ACCCGACGCAACCAGATACCCTGTTGGACTCCATCCAACGCAGTTCGTAGTAAGAGCGAAAGAGATCAAGAAAAGGCTCTACCCCAATGTAGGCCTCGCA[G/A]
AGATGAGCAAAGATGCTAAGAAAGGCGATAGAATTGGGGTTCAAATGGAGAAGAGAAAGACCATAGAAGTTCAAAACCAGGAGAAGAAATTCGGAAGACG
| 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 | 75.50% | 6.50% | 4.32% | 13.75% | NA |
| All Indica | 2759 | 60.30% | 10.90% | 7.00% | 21.86% | NA |
| All Japonica | 1512 | 98.70% | 0.00% | 0.07% | 1.19% | NA |
| Aus | 269 | 88.50% | 0.40% | 2.97% | 8.18% | NA |
| Indica I | 595 | 45.90% | 14.50% | 7.56% | 32.10% | NA |
| Indica II | 465 | 57.80% | 11.60% | 9.89% | 20.65% | NA |
| Indica III | 913 | 68.80% | 8.40% | 4.38% | 18.40% | NA |
| Indica Intermediate | 786 | 62.70% | 10.60% | 7.89% | 18.83% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208919948 | C -> DEL | LOC_Os12g15620.1 | N | frameshift_variant | Average:27.91; most accessible tissue: Minghui63 flag leaf, score: 66.004 | N | N | N | N |
| vg1208919948 | C -> T | LOC_Os12g15620.1 | synonymous_variant ; p.Leu91Leu; LOW | synonymous_codon | Average:27.91; most accessible tissue: Minghui63 flag leaf, score: 66.004 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208919948 | 2.14E-06 | 1.70E-10 | mr1707_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 |
| vg1208919948 | NA | 6.15E-06 | mr1707_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 |