| Variant ID: vg1001300112 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1300112 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTCTAAGCATGACTAAGCATCTATAATAATCATATAGCTGAACCAAACCAATATATAAGGTTCTAGCTAATCAAATTATAACCCATAGGAAAATAAAGT[T/C]
ATCTTCGGCCATAATTAAATGGGAAAGGCTCACCACCCGGTGACATTCGAAAATAATGTATAAGTTCAAATAAAACATTAGCTTTAAACGGGTTCAACAT
ATGTTGAACCCGTTTAAAGCTAATGTTTTATTTGAACTTATACATTATTTTCGAATGTCACCGGGTGGTGAGCCTTTCCCATTTAATTATGGCCGAAGAT[A/G]
ACTTTATTTTCCTATGGGTTATAATTTGATTAGCTAGAACCTTATATATTGGTTTGGTTCAGCTATATGATTATTATAGATGCTTAGTCATGCTTAGAAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.70% | 21.40% | 14.92% | 16.04% | NA |
| All Indica | 2759 | 65.60% | 4.20% | 21.24% | 8.92% | NA |
| All Japonica | 1512 | 8.50% | 56.10% | 5.03% | 30.36% | NA |
| Aus | 269 | 93.30% | 1.50% | 1.49% | 3.72% | NA |
| Indica I | 595 | 66.40% | 9.70% | 10.59% | 13.28% | NA |
| Indica II | 465 | 50.10% | 4.70% | 34.84% | 10.32% | NA |
| Indica III | 913 | 68.90% | 1.50% | 23.44% | 6.13% | NA |
| Indica Intermediate | 786 | 70.40% | 2.90% | 18.70% | 8.02% | NA |
| Temperate Japonica | 767 | 1.30% | 85.40% | 3.13% | 10.17% | NA |
| Tropical Japonica | 504 | 20.40% | 20.00% | 5.75% | 53.77% | NA |
| Japonica Intermediate | 241 | 6.60% | 38.20% | 9.54% | 45.64% | NA |
| VI/Aromatic | 96 | 20.80% | 20.80% | 23.96% | 34.38% | NA |
| Intermediate | 90 | 47.80% | 23.30% | 17.78% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001300112 | T -> C | LOC_Os10g03090.1 | upstream_gene_variant ; 877.0bp to feature; MODIFIER | silent_mutation | Average:32.035; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| vg1001300112 | T -> C | LOC_Os10g03080-LOC_Os10g03090 | intergenic_region ; MODIFIER | silent_mutation | Average:32.035; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| vg1001300112 | T -> DEL | N | N | silent_mutation | Average:32.035; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001300112 | NA | 6.96E-06 | mr1179 | 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 |
| vg1001300112 | 5.71E-06 | 1.05E-08 | mr1205 | 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 |
| vg1001300112 | NA | 1.52E-07 | mr1206 | 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 |
| vg1001300112 | NA | 5.85E-07 | mr1403 | 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 |
| vg1001300112 | NA | 5.43E-09 | mr1570 | 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 |
| vg1001300112 | NA | 1.69E-07 | mr1723 | 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 |