| Variant ID: vg0413193204 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 13193204 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGGCTGCTTAGCGATGCGGGCACTCCGACGTTTGGCGCCAGTGTTGTACTGCTTGCGGAGCTTGACACGGCGGCCGACTGCCACCTTTCTTATTGGCGG[C/T]
GGCATGGGGATGACCGCCATTGGTGGTGTTGCAAACAGGCTGTCCAGGGCGAGCTGTGCTGGCGTCACTGACGTCGTTGTTGTCGTCGTCGCACCGCTTG
CAAGCGGTGCGACGACGACAACAACGACGTCAGTGACGCCAGCACAGCTCGCCCTGGACAGCCTGTTTGCAACACCACCAATGGCGGTCATCCCCATGCC[G/A]
CCGCCAATAAGAAAGGTGGCAGTCGGCCGCCGTGTCAAGCTCCGCAAGCAGTACAACACTGGCGCCAAACGTCGGAGTGCCCGCATCGCTAAGCAGCCGG
| 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 | 48.40% | 9.40% | 1.95% | 40.25% | NA |
| All Indica | 2759 | 24.60% | 15.60% | 2.75% | 57.01% | NA |
| All Japonica | 1512 | 96.70% | 0.00% | 0.26% | 3.04% | NA |
| Aus | 269 | 2.20% | 3.30% | 3.72% | 90.71% | NA |
| Indica I | 595 | 31.90% | 1.50% | 2.18% | 64.37% | NA |
| Indica II | 465 | 27.70% | 6.70% | 2.80% | 62.80% | NA |
| Indica III | 913 | 24.30% | 30.90% | 3.50% | 41.29% | NA |
| Indica Intermediate | 786 | 17.60% | 13.90% | 2.29% | 66.28% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 0.52% | 2.48% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.00% | 6.64% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 63.30% | 3.30% | 1.11% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0413193204 | C -> DEL | LOC_Os04g23200.1 | N | frameshift_variant | Average:12.641; most accessible tissue: Callus, score: 65.499 | N | N | N | N |
| vg0413193204 | C -> T | LOC_Os04g23200.1 | synonymous_variant ; p.Pro648Pro; LOW | synonymous_codon | Average:12.641; most accessible tissue: Callus, score: 65.499 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0413193204 | 7.00E-06 | NA | mr1113_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 |
| vg0413193204 | 7.15E-06 | NA | mr1114_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 |
| vg0413193204 | NA | 1.52E-07 | mr1144_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 |
| vg0413193204 | 5.63E-06 | NA | mr1247_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 |