| Variant ID: vg0138838250 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 38838250 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 99. )
CCTTGTACGTAAAAATTTCTTAGTGCATCTGCAACAATCAATGTTTTATGCGTGTCTCCCTCAATCTAAAAGTCTAAGTCCTATTTATGGTGGTCACATC[A/G]
GATACATGGACACACATTATAGATTCCGCTAAAAAACTACGAAACGAATTTATTAAGCCTAATTAATCCATCATTAGCAAATATTTATTATAGCACCACA
TGTGGTGCTATAATAAATATTTGCTAATGATGGATTAATTAGGCTTAATAAATTCGTTTCGTAGTTTTTTAGCGGAATCTATAATGTGTGTCCATGTATC[T/C]
GATGTGACCACCATAAATAGGACTTAGACTTTTAGATTGAGGGAGACACGCATAAAACATTGATTGTTGCAGATGCACTAAGAAATTTTTACGTACAAGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.50% | 16.50% | 1.80% | 61.24% | NA |
| All Indica | 2759 | 1.00% | 1.20% | 2.43% | 95.36% | NA |
| All Japonica | 1512 | 60.40% | 31.60% | 0.93% | 7.01% | NA |
| Aus | 269 | 0.00% | 63.20% | 0.00% | 36.80% | NA |
| Indica I | 595 | 1.20% | 0.50% | 2.52% | 95.80% | NA |
| Indica II | 465 | 1.10% | 0.40% | 3.23% | 95.27% | NA |
| Indica III | 913 | 0.80% | 1.30% | 1.10% | 96.82% | NA |
| Indica Intermediate | 786 | 1.10% | 2.00% | 3.44% | 93.38% | NA |
| Temperate Japonica | 767 | 65.10% | 30.90% | 1.17% | 2.87% | NA |
| Tropical Japonica | 504 | 48.20% | 37.50% | 0.60% | 13.69% | NA |
| Japonica Intermediate | 241 | 71.40% | 21.60% | 0.83% | 6.22% | NA |
| VI/Aromatic | 96 | 0.00% | 84.40% | 0.00% | 15.62% | NA |
| Intermediate | 90 | 28.90% | 18.90% | 4.44% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0138838250 | A -> G | LOC_Os01g66870.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.897; most accessible tissue: Callus, score: 85.603 | N | N | N | N |
| vg0138838250 | A -> DEL | N | N | silent_mutation | Average:12.897; most accessible tissue: Callus, score: 85.603 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0138838250 | NA | 1.87E-21 | Awn_length | 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 |
| vg0138838250 | NA | 5.26E-08 | mr1221_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 |