| Variant ID: vg1126519704 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26519704 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTATCAGTGATTCATAATATCTGGTCGAGTTAGGCAAATTGATCTCACAATAAAATCAGTCACCTGAAATTAACACAAACATAGGATGTTGTGCGATCG[C/T]
GTCGGCCCCAACAAATTCATCAACAGCTCTATACCTTCGTAGCATAGGCTGTGTTTAGTTGGTGCCAAAATTGGAAGTTTGGTTGAAATTAGAACGATGT
ACATCGTTCTAATTTCAACCAAACTTCCAATTTTGGCACCAACTAAACACAGCCTATGCTACGAAGGTATAGAGCTGTTGATGAATTTGTTGGGGCCGAC[G/A]
CGATCGCACAACATCCTATGTTTGTGTTAATTTCAGGTGACTGATTTTATTGTGAGATCAATTTGCCTAACTCGACCAGATATTATGAATCACTGATAAA
| 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 | 53.20% | 7.50% | 5.50% | 33.81% | NA |
| All Indica | 2759 | 59.20% | 8.80% | 7.97% | 23.99% | NA |
| All Japonica | 1512 | 47.20% | 6.50% | 1.98% | 44.31% | NA |
| Aus | 269 | 37.90% | 2.20% | 2.23% | 57.62% | NA |
| Indica I | 595 | 47.90% | 0.00% | 8.24% | 43.87% | NA |
| Indica II | 465 | 52.30% | 3.40% | 19.78% | 24.52% | NA |
| Indica III | 913 | 65.30% | 18.90% | 2.19% | 13.58% | NA |
| Indica Intermediate | 786 | 64.90% | 6.90% | 7.51% | 20.74% | NA |
| Temperate Japonica | 767 | 65.40% | 12.30% | 2.35% | 19.95% | NA |
| Tropical Japonica | 504 | 23.80% | 0.60% | 1.79% | 73.81% | NA |
| Japonica Intermediate | 241 | 38.20% | 0.40% | 1.24% | 60.17% | NA |
| VI/Aromatic | 96 | 22.90% | 0.00% | 0.00% | 77.08% | NA |
| Intermediate | 90 | 44.40% | 10.00% | 4.44% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126519704 | C -> T | LOC_Os11g43914.1 | upstream_gene_variant ; 1645.0bp to feature; MODIFIER | silent_mutation | Average:55.555; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg1126519704 | C -> T | LOC_Os11g43910.1 | downstream_gene_variant ; 4896.0bp to feature; MODIFIER | silent_mutation | Average:55.555; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg1126519704 | C -> T | LOC_Os11g43920.1 | downstream_gene_variant ; 1201.0bp to feature; MODIFIER | silent_mutation | Average:55.555; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg1126519704 | C -> T | LOC_Os11g43920-LOC_Os11g43934 | intergenic_region ; MODIFIER | silent_mutation | Average:55.555; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg1126519704 | C -> DEL | N | N | silent_mutation | Average:55.555; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126519704 | NA | 1.82E-07 | mr1585 | 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 |
| vg1126519704 | NA | 4.49E-06 | mr1693_2 | 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 |
| vg1126519704 | NA | 3.35E-06 | mr1693_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 |
| vg1126519704 | 6.32E-06 | NA | mr1888_2 | 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 |