| Variant ID: vg0114081823 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 14081823 |
| Reference Allele: CATATGGGTTCAAAA | Alternative Allele: TATATGGGTTCAAAA,C |
| Primary Allele: CATATGGGTTCAAAA | Secondary Allele: TATATGGGTTCAAAA |
Inferred Ancestral Allele: Not determined.
ATTAAACACTATTACAAAATCCCTAATAGGGGACGCCCTTCTATGTGTTGGTTCATCCAAAACCGGCACATATAAGGCTTTCTATGCTTTTTCAACCCCT[CATATGGGTTCAAAA/TATATGGGTTCAAAA,C]
ATAAAAAAACCGACACTAATATAAGTGCTAGTTTTTCTAATAAACTGGCACTTTCATGTAGGATAAAAGTGTTAAAAAAAGTCACTTTTAGGGATAGAGC
GCTCTATCCCTAAAAGTGACTTTTTTTAACACTTTTATCCTACATGAAAGTGCCAGTTTATTAGAAAAACTAGCACTTATATTAGTGTCGGTTTTTTTAT[TTTTGAACCCATATG/TTTTGAACCCATATA,G]
AGGGGTTGAAAAAGCATAGAAAGCCTTATATGTGCCGGTTTTGGATGAACCAACACATAGAAGGGCGTCCCCTATTAGGGATTTTGTAATAGTGTTTAAT
| Populations | Population Size | Frequency of CATATGGGTTCAAAA(primary allele) | Frequency of TATATGGGTTCAAAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.70% | 5.80% | 0.34% | 0.25% | NA |
| All Indica | 2759 | 93.00% | 6.00% | 0.58% | 0.43% | NA |
| All Japonica | 1512 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.10% | 13.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 95.30% | 2.40% | 1.51% | 0.86% | NA |
| Indica III | 913 | 98.00% | 1.00% | 0.33% | 0.66% | NA |
| Indica Intermediate | 786 | 91.10% | 8.00% | 0.64% | 0.25% | NA |
| Temperate Japonica | 767 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 89.50% | 10.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 61.50% | 38.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114081823 | CATATGGGTTCAAAA -> DEL | N | N | silent_mutation | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> C | LOC_Os01g24990.1 | upstream_gene_variant ; 4010.0bp to feature; MODIFIER | N | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> C | LOC_Os01g24980.1 | downstream_gene_variant ; 1108.0bp to feature; MODIFIER | N | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> C | LOC_Os01g24980.2 | downstream_gene_variant ; 1108.0bp to feature; MODIFIER | N | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> C | LOC_Os01g24980-LOC_Os01g24990 | intergenic_region ; MODIFIER | N | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> TATATGGGTTCAAAA | LOC_Os01g24990.1 | upstream_gene_variant ; 4011.0bp to feature; MODIFIER | silent_mutation | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> TATATGGGTTCAAAA | LOC_Os01g24980.1 | downstream_gene_variant ; 1107.0bp to feature; MODIFIER | silent_mutation | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> TATATGGGTTCAAAA | LOC_Os01g24980.2 | downstream_gene_variant ; 1107.0bp to feature; MODIFIER | silent_mutation | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| vg0114081823 | CATATGGGTTCAAAA -> TATATGGGTTCAAAA | LOC_Os01g24980-LOC_Os01g24990 | intergenic_region ; MODIFIER | silent_mutation | Average:66.924; most accessible tissue: Minghui63 root, score: 81.325 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114081823 | 8.28E-07 | 1.50E-09 | mr1064 | Ind_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 |
| vg0114081823 | NA | 8.37E-06 | mr1125 | Ind_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 |
| vg0114081823 | NA | 1.23E-07 | mr1136 | Ind_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 |
| vg0114081823 | NA | 3.11E-07 | mr1534 | Ind_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 |
| vg0114081823 | NA | 4.34E-07 | mr1679 | Ind_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 |
| vg0114081823 | 2.99E-07 | 1.82E-09 | mr1741 | Ind_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 |
| vg0114081823 | NA | 6.91E-06 | mr1798 | Ind_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 |
| vg0114081823 | NA | 4.51E-07 | mr1458_2 | Ind_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 |