| Variant ID: vg0305665264 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 5665264 |
| Reference Allele: GTT | Alternative Allele: G,ATT |
| Primary Allele: GTT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGTAACCCTTTGTAGTCTCGGTTTTTCAACCGGGACGGACTAAAGATCGCAATCTTTAGTCCCGATTCAAATAATCGGGACTAAAAATATGGTCCCGGTT[GTT/G,ATT]
GTTACCAACCGGGACTAAAAAAGTTTTGTTTGTTTTCTTTTCCTTTCATCCGGTTGGCCTTTTTCCTTTTGTATTGTTCTTTAGCTTTCGCTCGTGGATC
GATCCACGAGCGAAAGCTAAAGAACAATACAAAAGGAAAAAGGCCAACCGGATGAAAGGAAAAGAAAACAAACAAAACTTTTTTAGTCCCGGTTGGTAAC[AAC/C,AAT]
AACCGGGACCATATTTTTAGTCCCGATTATTTGAATCGGGACTAAAGATTGCGATCTTTAGTCCGTCCCGGTTGAAAAACCGAGACTACAAAGGGTTACC
| Populations | Population Size | Frequency of GTT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.80% | 11.70% | 1.50% | 52.98% | ATT: 0.02% |
| All Indica | 2759 | 10.00% | 0.30% | 1.88% | 87.75% | ATT: 0.04% |
| All Japonica | 1512 | 63.90% | 34.30% | 0.99% | 0.79% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.00% | 1.12% | NA |
| Indica I | 595 | 0.70% | 0.00% | 1.85% | 97.48% | NA |
| Indica II | 465 | 14.20% | 0.20% | 1.51% | 84.09% | NA |
| Indica III | 913 | 13.30% | 0.20% | 1.97% | 84.45% | ATT: 0.11% |
| Indica Intermediate | 786 | 10.80% | 0.80% | 2.04% | 86.39% | NA |
| Temperate Japonica | 767 | 97.10% | 0.80% | 0.65% | 1.43% | NA |
| Tropical Japonica | 504 | 9.70% | 88.90% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 71.40% | 27.00% | 1.24% | 0.41% | NA |
| VI/Aromatic | 96 | 62.50% | 6.20% | 1.04% | 30.21% | NA |
| Intermediate | 90 | 32.20% | 21.10% | 3.33% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0305665264 | GTT -> DEL | N | N | silent_mutation | Average:78.356; most accessible tissue: Minghui63 young leaf, score: 93.727 | N | N | N | N |
| vg0305665264 | GTT -> ATT | LOC_Os03g11020.1 | upstream_gene_variant ; 4659.0bp to feature; MODIFIER | silent_mutation | Average:78.356; most accessible tissue: Minghui63 young leaf, score: 93.727 | N | N | N | N |
| vg0305665264 | GTT -> ATT | LOC_Os03g11010-LOC_Os03g11020 | intergenic_region ; MODIFIER | silent_mutation | Average:78.356; most accessible tissue: Minghui63 young leaf, score: 93.727 | N | N | N | N |
| vg0305665264 | GTT -> G | LOC_Os03g11020.1 | upstream_gene_variant ; 4658.0bp to feature; MODIFIER | silent_mutation | Average:78.356; most accessible tissue: Minghui63 young leaf, score: 93.727 | N | N | N | N |
| vg0305665264 | GTT -> G | LOC_Os03g11010-LOC_Os03g11020 | intergenic_region ; MODIFIER | silent_mutation | Average:78.356; most accessible tissue: Minghui63 young leaf, score: 93.727 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0305665264 | NA | 5.84E-23 | mr1020 | 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 |
| vg0305665264 | NA | 2.14E-20 | mr1021 | 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 |
| vg0305665264 | NA | 6.93E-27 | mr1076 | 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 |
| vg0305665264 | NA | 2.30E-43 | mr1082 | 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 |
| vg0305665264 | NA | 7.22E-24 | mr1083 | 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 |
| vg0305665264 | NA | 1.21E-32 | mr1085 | 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 |
| vg0305665264 | NA | 3.64E-34 | mr1086 | 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 |
| vg0305665264 | NA | 2.96E-57 | mr1087 | 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 |
| vg0305665264 | NA | 9.65E-62 | mr1103 | 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 |
| vg0305665264 | NA | 3.21E-35 | mr1104 | 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 |
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