| Variant ID: vg1010594417 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 10594417 |
| Reference Allele: T | Alternative Allele: C,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCCAAACATACACCATCGAAGTAGTGTTAATAGCATATCTCAAATCTGCAGGAAGCCATCTGACATCGATCCTTCTAGGAAAGACTAAACCGACTAGCA[T/C,A]
GGAGACTGGTCCTACGACCTCCACAGAAACCGGGCCGACCGCCGAAAATCGCCTGACTAGTAGTCAACCAGCGACCGATAATATAGAGGCCAGCAATGAG
CTCATTGCTGGCCTCTATATTATCGGTCGCTGGTTGACTACTAGTCAGGCGATTTTCGGCGGTCGGCCCGGTTTCTGTGGAGGTCGTAGGACCAGTCTCC[A/G,T]
TGCTAGTCGGTTTAGTCTTTCCTAGAAGGATCGATGTCAGATGGCTTCCTGCAGATTTGAGATATGCTATTAACACTACTTCGATGGTGTATGTTTGGCG
| 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 | 68.30% | 21.10% | 1.54% | 9.04% | A: 0.04% |
| All Indica | 2759 | 94.10% | 0.80% | 1.81% | 3.26% | A: 0.07% |
| All Japonica | 1512 | 15.30% | 62.60% | 0.93% | 21.16% | NA |
| Aus | 269 | 97.00% | 0.70% | 0.00% | 2.23% | NA |
| Indica I | 595 | 99.70% | 0.20% | 0.00% | 0.17% | NA |
| Indica II | 465 | 91.00% | 0.90% | 0.86% | 7.31% | NA |
| Indica III | 913 | 92.30% | 1.00% | 4.05% | 2.41% | A: 0.22% |
| Indica Intermediate | 786 | 93.80% | 0.90% | 1.15% | 4.20% | NA |
| Temperate Japonica | 767 | 15.40% | 79.50% | 0.52% | 4.56% | NA |
| Tropical Japonica | 504 | 8.10% | 46.20% | 1.98% | 43.65% | NA |
| Japonica Intermediate | 241 | 29.90% | 43.20% | 0.00% | 26.97% | NA |
| VI/Aromatic | 96 | 89.60% | 2.10% | 5.21% | 3.12% | NA |
| Intermediate | 90 | 57.80% | 28.90% | 4.44% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1010594417 | T -> C | LOC_Os10g20910.1 | upstream_gene_variant ; 3007.0bp to feature; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> C | LOC_Os10g20900.1 | downstream_gene_variant ; 4910.0bp to feature; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> C | LOC_Os10g20930.1 | downstream_gene_variant ; 2067.0bp to feature; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> C | LOC_Os10g20920.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> A | LOC_Os10g20910.1 | upstream_gene_variant ; 3007.0bp to feature; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> A | LOC_Os10g20900.1 | downstream_gene_variant ; 4910.0bp to feature; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> A | LOC_Os10g20930.1 | downstream_gene_variant ; 2067.0bp to feature; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> A | LOC_Os10g20920.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| vg1010594417 | T -> DEL | N | N | silent_mutation | Average:49.213; most accessible tissue: Zhenshan97 young leaf, score: 81.841 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1010594417 | NA | 1.98E-07 | mr1690 | 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 |
| vg1010594417 | NA | 9.60E-10 | mr1576_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 |
| vg1010594417 | 9.84E-06 | 1.75E-10 | mr1660_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 |
| vg1010594417 | 7.04E-07 | 4.28E-07 | mr1660_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 |