| Variant ID: vg0520363169 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 20363169 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 272. )
AGCGACTGATCGTAAAAGGGGATTCCGAACTAGTCGCAAACCAGGTGCACAAAGACTACAAGTGCTCTTGCCCCGAGTTGTCCAAGTATCTCGCAGAAGT[C/T]
AGGAAGCTGGAAAAAAGATTTGATGGGATCGAGGTCCGACACGTATATCACAAGGACAACATCAAGCCGGATGATCTAGTACGGCGTGCGTCCAGATGAG
CTCATCTGGACGCACGCCGTACTAGATCATCCGGCTTGATGTTGTCCTTGTGATATACGTGTCGGACCTCGATCCCATCAAATCTTTTTTCCAGCTTCCT[G/A]
ACTTCTGCGAGATACTTGGACAACTCGGGGCAAGAGCACTTGTAGTCTTTGTGCACCTGGTTTGCGACTAGTTCGGAATCCCCTTTTACGATCAGTCGCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.40% | 41.40% | 0.25% | 0.99% | NA |
| All Indica | 2759 | 94.40% | 3.70% | 0.36% | 1.56% | NA |
| All Japonica | 1512 | 2.60% | 97.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 7.10% | 91.10% | 0.37% | 1.49% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 96.10% | 3.20% | 0.22% | 0.43% | NA |
| Indica III | 913 | 93.50% | 2.60% | 0.22% | 3.61% | NA |
| Indica Intermediate | 786 | 90.80% | 7.40% | 0.76% | 1.02% | NA |
| Temperate Japonica | 767 | 3.80% | 96.10% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 1.80% | 98.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 52.20% | 47.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0520363169 | C -> T | LOC_Os05g34350.1 | synonymous_variant ; p.Val860Val; LOW | synonymous_codon | Average:40.29; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 | N | N | N | N |
| vg0520363169 | C -> DEL | LOC_Os05g34350.1 | N | frameshift_variant | Average:40.29; most accessible tissue: Zhenshan97 flag leaf, score: 67.31 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0520363169 | NA | 3.74E-06 | Awn_length | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0520363169 | NA | 2.88E-26 | mr1037 | 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 |
| vg0520363169 | NA | 2.69E-07 | mr1053 | 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 |
| vg0520363169 | NA | 3.18E-06 | mr1058 | 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 |
| vg0520363169 | NA | 5.05E-54 | mr1068 | 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 |
| vg0520363169 | NA | 3.16E-37 | mr1094 | 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 |
| vg0520363169 | NA | 5.73E-53 | mr1096 | 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 |
| vg0520363169 | NA | 1.85E-48 | mr1109 | 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 |
| vg0520363169 | NA | 3.46E-39 | mr1110 | 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 |
| vg0520363169 | 7.49E-06 | NA | mr1110 | 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 |
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