| Variant ID: vg0815562300 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15562300 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATAGATGGAACATTTTTGACAGGTAAATACCACTGGCAGTGGTACCTGCTCGGGCTACCACTGGCAGGAGCCCCAGTTGGTCCCGTGGACGGTGTTTTT[G/T]
GCTGGAAGGAGGATATCACCGTGCGCTTCGAGCACGTGATGCGCCTTCCACACCTAGGACCGCCCAACACCCTTCCCCCGTACTCTACCGTCGGGCCTAG
CTAGGCCCGACGGTAGAGTACGGGGGAAGGGTGTTGGGCGGTCCTAGGTGTGGAAGGCGCATCACGTGCTCGAAGCGCACGGTGATATCCTCCTTCCAGC[C/A]
AAAAACACCGTCCACGGGACCAACTGGGGCTCCTGCCAGTGGTAGCCCGAGCAGGTACCACTGCCAGTGGTATTTACCTGTCAAAAATGTTCCATCTATG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.20% | 6.40% | 0.19% | 0.19% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 82.40% | 16.80% | 0.40% | 0.40% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 55.20% | 42.70% | 0.99% | 1.19% | NA |
| Japonica Intermediate | 241 | 88.00% | 11.60% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 56.20% | 39.60% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 88.90% | 8.90% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815562300 | G -> T | LOC_Os08g25570.1 | downstream_gene_variant ; 3148.0bp to feature; MODIFIER | silent_mutation | Average:57.898; most accessible tissue: Minghui63 flag leaf, score: 75.722 | N | N | N | N |
| vg0815562300 | G -> T | LOC_Os08g25580.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.898; most accessible tissue: Minghui63 flag leaf, score: 75.722 | N | N | N | N |
| vg0815562300 | G -> DEL | N | N | silent_mutation | Average:57.898; most accessible tissue: Minghui63 flag leaf, score: 75.722 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0815562300 | NA | 7.05E-08 | mr1746 | 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 |
| vg0815562300 | NA | 3.50E-06 | mr1232_2 | 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 |
| vg0815562300 | 2.21E-06 | 2.21E-06 | mr1424_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 |
| vg0815562300 | NA | 5.92E-06 | mr1557_2 | 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 |
| vg0815562300 | 9.35E-06 | 9.35E-06 | mr1562_2 | 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 |
| vg0815562300 | NA | 4.05E-06 | mr1884_2 | 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 |