| Variant ID: vg1020508138 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 20508138 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGAAGCTCATGAGTCCGCCTACTCCATCTATCCAGGAAGTACGAAGATGTACCAGGATATCAAGGCATATTTCTGGTGGGTTGGAATGAAGCGAGATGT[C/T]
GCAGAATACGTAGCCCTTTGTGACATTTGCCAGAGAGTCAAGGCAGAGCATCAGAGGCCAGCTGGTCTGCTGCAACCCCTACCGATTCCCGAGTGGAAAT
ATTTCCACTCGGGAATCGGTAGGGGTTGCAGCAGACCAGCTGGCCTCTGATGCTCTGCCTTGACTCTCTGGCAAATGTCACAAAGGGCTACGTATTCTGC[G/A]
ACATCTCGCTTCATTCCAACCCACCAGAAATATGCCTTGATATCCTGGTACATCTTCGTACTTCCTGGATAGATGGAGTAGGCGGACTCATGAGCTTCTT
| 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 | 89.70% | 7.80% | 0.36% | 2.22% | NA |
| All Indica | 2759 | 99.80% | 0.10% | 0.00% | 0.11% | NA |
| All Japonica | 1512 | 68.60% | 23.70% | 1.06% | 6.61% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.10% | 0.40% | 0.00% | 0.43% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 89.00% | 9.50% | 0.52% | 0.91% | NA |
| Tropical Japonica | 504 | 33.70% | 46.60% | 2.18% | 17.46% | NA |
| Japonica Intermediate | 241 | 76.30% | 21.20% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 5.60% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1020508138 | C -> T | LOC_Os10g38370.1 | synonymous_variant ; p.Val1432Val; LOW | synonymous_codon | Average:22.682; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
| vg1020508138 | C -> DEL | LOC_Os10g38370.1 | N | frameshift_variant | Average:22.682; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1020508138 | NA | 8.68E-06 | mr1267_2 | Jap_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 |
| vg1020508138 | 5.20E-06 | 5.20E-06 | mr1312_2 | Jap_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 |
| vg1020508138 | 4.89E-06 | 1.80E-07 | mr1397_2 | Jap_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 |
| vg1020508138 | 5.56E-06 | 5.55E-06 | mr1663_2 | Jap_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 |
| vg1020508138 | NA | 3.20E-06 | mr1833_2 | Jap_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 |
| vg1020508138 | 4.74E-06 | 4.74E-06 | mr1843_2 | Jap_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 |
| vg1020508138 | 4.62E-06 | 4.62E-06 | mr1847_2 | Jap_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 |