| Variant ID: vg0920930440 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 20930440 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 313. )
AATCTACCTTGTGTTGTTGGTGTAGATGATTTCAACCTATGGTTTTGGTGAATAACAATCATAACGCTGTAGAACAACTTGTAGTAAACCATGACAAGAA[T/A]
ACCTTCCTTCCCATTTCCCCAAGATTAGCTCTTGTATAGCACTTGAATATTTGGCTAGCAATCCATTATTCTCAATCCTACCTTGTAGGTGTTGTTGTAG
CTACAACAACACCTACAAGGTAGGATTGAGAATAATGGATTGCTAGCCAAATATTCAAGTGCTATACAAGAGCTAATCTTGGGGAAATGGGAAGGAAGGT[A/T]
TTCTTGTCATGGTTTACTACAAGTTGTTCTACAGCGTTATGATTGTTATTCACCAAAACCATAGGTTGAAATCATCTACACCAACAACACAAGGTAGATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.20% | 37.60% | 1.16% | 0.00% | NA |
| All Indica | 2759 | 63.20% | 36.10% | 0.72% | 0.00% | NA |
| All Japonica | 1512 | 60.00% | 37.80% | 2.18% | 0.00% | NA |
| Aus | 269 | 68.80% | 31.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 89.40% | 9.60% | 1.01% | 0.00% | NA |
| Indica II | 465 | 42.80% | 56.80% | 0.43% | 0.00% | NA |
| Indica III | 913 | 56.80% | 42.90% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 62.80% | 35.90% | 1.27% | 0.00% | NA |
| Temperate Japonica | 767 | 83.80% | 13.30% | 2.87% | 0.00% | NA |
| Tropical Japonica | 504 | 33.90% | 65.50% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 38.60% | 58.10% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 20.80% | 78.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 41.10% | 57.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0920930440 | T -> A | LOC_Os09g36270.1 | intron_variant ; MODIFIER | silent_mutation | Average:50.416; most accessible tissue: Callus, score: 85.925 | N | N | N | N |
| vg0920930440 | T -> A | LOC_Os09g36270.2 | intron_variant ; MODIFIER | silent_mutation | Average:50.416; most accessible tissue: Callus, score: 85.925 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0920930440 | NA | 5.53E-11 | Heading_date | Jap_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 |
| vg0920930440 | NA | 7.63E-07 | mr1125 | 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 |
| vg0920930440 | NA | 6.53E-06 | mr1548 | 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 |
| vg0920930440 | NA | 3.13E-08 | mr1570 | 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 |
| vg0920930440 | NA | 7.02E-10 | mr1629_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 |
| vg0920930440 | NA | 4.42E-06 | mr1968_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 |