| Variant ID: vg1001890148 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1890148 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.02, others allele: 0.00, population size: 186. )
TTTTAGATAATGGAAGCTTTTATTAAACTCAGTCAATTACATCAAGGTGATACAATTATCCTGAGAACACTTCCGGCCTCTGCATAACTAAGATGCACAC[C/A]
GCCGAACAAACAAAACGACACTCGAAAGGAAAAAAGAATGACATGGAGTATTGAGGACCATCAATCTAACGACTAAATTGCCACTCATGAACAACTCCTT
AAGGAGTTGTTCATGAGTGGCAATTTAGTCGTTAGATTGATGGTCCTCAATACTCCATGTCATTCTTTTTTCCTTTCGAGTGTCGTTTTGTTTGTTCGGC[G/T]
GTGTGCATCTTAGTTATGCAGAGGCCGGAAGTGTTCTCAGGATAATTGTATCACCTTGATGTAATTGACTGAGTTTAATAAAAGCTTCCATTATCTAAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.10% | 34.70% | 4.46% | 4.78% | NA |
| All Indica | 2759 | 83.90% | 3.80% | 4.60% | 7.76% | NA |
| All Japonica | 1512 | 7.30% | 92.10% | 0.46% | 0.20% | NA |
| Aus | 269 | 68.00% | 1.90% | 27.51% | 2.60% | NA |
| Indica I | 595 | 72.10% | 3.50% | 4.54% | 19.83% | NA |
| Indica II | 465 | 87.50% | 3.90% | 2.80% | 5.81% | NA |
| Indica III | 913 | 88.50% | 2.30% | 6.68% | 2.52% | NA |
| Indica Intermediate | 786 | 85.20% | 5.60% | 3.31% | 5.85% | NA |
| Temperate Japonica | 767 | 2.60% | 96.70% | 0.39% | 0.26% | NA |
| Tropical Japonica | 504 | 14.90% | 84.90% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 6.20% | 92.10% | 1.24% | 0.41% | NA |
| VI/Aromatic | 96 | 9.40% | 90.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 37.80% | 56.70% | 3.33% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001890148 | C -> A | LOC_Os10g04090.1 | 3_prime_UTR_variant ; 1200.0bp to feature; MODIFIER | silent_mutation | Average:35.125; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| vg1001890148 | C -> A | LOC_Os10g04074.1 | downstream_gene_variant ; 2398.0bp to feature; MODIFIER | silent_mutation | Average:35.125; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| vg1001890148 | C -> DEL | N | N | silent_mutation | Average:35.125; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001890148 | NA | 1.01E-07 | mr1162 | 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 |
| vg1001890148 | 5.74E-06 | NA | mr1540 | 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 |
| vg1001890148 | NA | 1.56E-10 | mr1630 | 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 |
| vg1001890148 | 8.51E-07 | 8.51E-07 | mr1630 | 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 |
| vg1001890148 | NA | 1.65E-17 | mr1842 | 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 |