| Variant ID: vg1013680813 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 13680813 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.00, others allele: 0.00, population size: 286. )
CAAGCAACCTGGTAACGACATCGATGTGTACCTAAGACCACTGGTCGAAGATCTTAAACTGTTGTGGAAAAAGGAAGGTGTCCCCGTGTGGGATGAGGAC[A/T]
AACAGGAGGAGTTTAACCTACGAGCGCTGTTGTTCGTAACCATCAACGATTGGCCTGCACTTAGCAACCTTTCCGGGCAGTCCAACAAGGGGTACAAGGC
GCCTTGTACCCCTTGTTGGACTGCCCGGAAAGGTTGCTAAGTGCAGGCCAATCGTTGATGGTTACGAACAACAGCGCTCGTAGGTTAAACTCCTCCTGTT[T/A]
GTCCTCATCCCACACGGGGACACCTTCCTTTTTCCACAACAGTTTAAGATCTTCGACCAGTGGTCTTAGGTACACATCGATGTCGTTACCAGGTTGCTTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.30% | 41.90% | 2.24% | 7.58% | NA |
| All Indica | 2759 | 28.90% | 69.50% | 1.63% | 0.00% | NA |
| All Japonica | 1512 | 72.30% | 0.70% | 3.70% | 23.28% | NA |
| Aus | 269 | 91.40% | 8.20% | 0.37% | 0.00% | NA |
| Indica I | 595 | 31.80% | 65.70% | 2.52% | 0.00% | NA |
| Indica II | 465 | 8.80% | 89.50% | 1.72% | 0.00% | NA |
| Indica III | 913 | 34.10% | 65.10% | 0.88% | 0.00% | NA |
| Indica Intermediate | 786 | 32.40% | 65.80% | 1.78% | 0.00% | NA |
| Temperate Japonica | 767 | 94.10% | 0.30% | 0.78% | 4.82% | NA |
| Tropical Japonica | 504 | 50.80% | 1.20% | 4.96% | 43.06% | NA |
| Japonica Intermediate | 241 | 47.70% | 1.20% | 10.37% | 40.66% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 27.80% | 4.44% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1013680813 | A -> T | LOC_Os10g26370.1 | N | stop_gained | Average:36.098; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| vg1013680813 | A -> DEL | LOC_Os10g26370.1 | N | frameshift_variant | Average:36.098; most accessible tissue: Minghui63 panicle, score: 56.842 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1013680813 | 2.00E-07 | NA | mr1533 | 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 |
| vg1013680813 | 1.51E-07 | 1.43E-10 | mr1533 | 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 |
| vg1013680813 | NA | 1.19E-06 | mr1980 | 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 |
| vg1013680813 | 2.51E-06 | NA | mr1533_2 | 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 |
| vg1013680813 | 1.04E-06 | 2.47E-12 | mr1533_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 |
| vg1013680813 | NA | 7.81E-07 | mr1980_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 |