| Variant ID: vg0402377935 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 2377935 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGAAGGGGGACTGGGAGATTAGTGCGCAGAACATTTCGCCCGCTCTTTGCGCGTGGCGAAAACAGTTCTGGCAGAAGGATGGTCGGTCCGCTGCCAAGG[C/T]
GCGCCTTTTGGAGCAACTAGCGAAGGCGGAGGCGGCAGACCGGTGCGAAGAAGAGGACGCAGCAGGCGAAGAGGTTGGAGGCGATGCCCAGGATCACCCA
TGGGTGATCCTGGGCATCGCCTCCAACCTCTTCGCCTGCTGCGTCCTCTTCTTCGCACCGGTCTGCCGCCTCCGCCTTCGCTAGTTGCTCCAAAAGGCGC[G/A]
CCTTGGCAGCGGACCGACCATCCTTCTGCCAGAACTGTTTTCGCCACGCGCAAAGAGCGGGCGAAATGTTCTGCGCACTAATCTCCCAGTCCCCCTTCGC
| 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 | 61.00% | 5.10% | 6.50% | 27.44% | NA |
| All Indica | 2759 | 61.70% | 0.10% | 6.81% | 31.42% | NA |
| All Japonica | 1512 | 60.70% | 14.60% | 5.56% | 19.11% | NA |
| Aus | 269 | 62.10% | 0.00% | 7.81% | 30.11% | NA |
| Indica I | 595 | 38.70% | 0.00% | 5.71% | 55.63% | NA |
| Indica II | 465 | 61.10% | 0.00% | 7.10% | 31.83% | NA |
| Indica III | 913 | 73.50% | 0.10% | 7.34% | 19.06% | NA |
| Indica Intermediate | 786 | 65.80% | 0.10% | 6.87% | 27.23% | NA |
| Temperate Japonica | 767 | 73.50% | 17.20% | 1.43% | 7.82% | NA |
| Tropical Japonica | 504 | 40.10% | 13.70% | 10.91% | 35.32% | NA |
| Japonica Intermediate | 241 | 63.10% | 8.30% | 7.47% | 21.16% | NA |
| VI/Aromatic | 96 | 39.60% | 7.30% | 9.38% | 43.75% | NA |
| Intermediate | 90 | 63.30% | 11.10% | 5.56% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0402377935 | C -> DEL | N | N | silent_mutation | Average:14.214; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0402377935 | C -> T | LOC_Os04g04930.1 | downstream_gene_variant ; 137.0bp to feature; MODIFIER | silent_mutation | Average:14.214; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0402377935 | C -> T | LOC_Os04g04940.1 | downstream_gene_variant ; 1530.0bp to feature; MODIFIER | silent_mutation | Average:14.214; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0402377935 | C -> T | LOC_Os04g04930-LOC_Os04g04940 | intergenic_region ; MODIFIER | silent_mutation | Average:14.214; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0402377935 | 1.58E-06 | NA | mr1543_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 |
| vg0402377935 | 5.14E-06 | NA | mr1742_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 |
| vg0402377935 | 1.72E-07 | NA | mr1871_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 |