| Variant ID: vg0804589533 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 4589533 |
| Reference Allele: CTGTG | Alternative Allele: CTGTGTGTGTGTGTG,GTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG |
| Primary Allele: CTGTG | Secondary Allele: GTGTG |
Inferred Ancestral Allele: Not determined.
TTCAGATTTTGCCTACTCGATAGCGTTGTTCTTGCTTAATTGCCTTGAACAAACTAGTGATGTTGAGTTGAAAATCTCCCTCCCTCTCCTCACTGTATCT[CTGTG/CTGTGTGTGTGTGTG,GTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTG,C,CTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG]
TGTGTGTGTGTGTGTGTGTGTGTGTGTTTATTAAATATGTTTATTTCTTTGTCAACTGTGAAGGTGTGGAAACATTCATTGCAAATATTTATAATTTGAA
TTCAAATTATAAATATTTGCAATGAATGTTTCCACACCTTCACAGTTGACAAAGAAATAAACATATTTAATAAACACACACACACACACACACACACACA[CACAG/CACACACACACACAG,CACAC,CACACACACACACACACACACACACAG,G,CACACACACACACACACACACACACACAG,CACACACACACACACAG]
AGATACAGTGAGGAGAGGGAGGGAGATTTTCAACTCAACATCACTAGTTTGTTCAAGGCAATTAAGCAAGAACAACGCTATCGAGTAGGCAAAATCTGAA
| Populations | Population Size | Frequency of CTGTG(primary allele) | Frequency of GTGTG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.10% | 16.00% | 17.31% | 1.65% | C: 13.88%; CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 9.42%; CTGTGTGTGTGTGTGTG: 6.92%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 3.00%; CTGTGTGTGTGTGTG: 1.69% |
| All Indica | 2759 | 33.00% | 7.20% | 21.42% | 2.79% | CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 14.72%; CTGTGTGTGTGTGTGTG: 11.63%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 4.86%; CTGTGTGTGTGTGTG: 2.65%; C: 1.74% |
| All Japonica | 1512 | 29.40% | 18.00% | 12.04% | 0.00% | C: 39.48%; CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.53%; CTGTGTGTGTGTGTG: 0.33%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.20%; CTGTGTGTGTGTGTGTG: 0.07% |
| Aus | 269 | 16.40% | 68.40% | 7.81% | 0.00% | CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 5.95%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 1.12%; CTGTGTGTGTGTGTGTG: 0.37% |
| Indica I | 595 | 33.30% | 0.00% | 41.85% | 0.00% | CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 15.29%; C: 4.87%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 4.20%; CTGTGTGTGTGTGTG: 0.34%; CTGTGTGTGTGTGTGTG: 0.17% |
| Indica II | 465 | 27.70% | 8.20% | 20.65% | 13.76% | CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 18.06%; CTGTGTGTGTGTGTGTG: 4.95%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 4.52%; C: 1.51%; CTGTGTGTGTGTGTG: 0.65% |
| Indica III | 913 | 35.60% | 6.10% | 9.31% | 0.11% | CTGTGTGTGTGTGTGTG: 24.42%; CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 12.60%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 6.02%; CTGTGTGTGTGTGTG: 5.70%; C: 0.11% |
| Indica Intermediate | 786 | 33.00% | 13.20% | 20.48% | 1.53% | CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 14.76%; CTGTGTGTGTGTGTGTG: 9.41%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 4.20%; CTGTGTGTGTGTGTG: 2.04%; C: 1.40% |
| Temperate Japonica | 767 | 43.50% | 12.30% | 13.43% | 0.00% | C: 30.12%; CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.52%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.13% |
| Tropical Japonica | 504 | 8.90% | 11.30% | 12.30% | 0.00% | C: 65.87%; CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.60%; CTGTGTGTGTGTGTG: 0.60%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.20%; CTGTGTGTGTGTGTGTG: 0.20% |
| Japonica Intermediate | 241 | 27.00% | 50.20% | 7.05% | 0.00% | C: 14.11%; CTGTGTGTGTGTGTG: 0.83%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.41%; CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 0.41% |
| VI/Aromatic | 96 | 6.20% | 87.50% | 4.17% | 0.00% | CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 2.08% |
| Intermediate | 90 | 20.00% | 21.10% | 22.22% | 1.11% | CTGTGTGTGTGTGTGTGTGTGTGTGTGTG: 14.44%; C: 12.22%; CTGTGTGTGTGTGTGTG: 4.44%; CTGTGTGTGTGTGTGTGTGTGTGTGTG: 2.22%; CTGTGTGTGTGTGTG: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804589533 | CTGTG -> C | LOC_Os08g08090.1 | upstream_gene_variant ; 4137.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> C | LOC_Os08g08084.1 | downstream_gene_variant ; 2465.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> C | LOC_Os08g08080.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> C | LOC_Os08g08080.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTG | LOC_Os08g08090.1 | upstream_gene_variant ; 4133.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTG | LOC_Os08g08084.1 | downstream_gene_variant ; 2461.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTG | LOC_Os08g08080.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTG | LOC_Os08g08080.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08090.1 | upstream_gene_variant ; 4133.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08084.1 | downstream_gene_variant ; 2461.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08080.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08080.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> DEL | N | N | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTG | LOC_Os08g08090.1 | upstream_gene_variant ; 4133.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTG | LOC_Os08g08084.1 | downstream_gene_variant ; 2461.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTG | LOC_Os08g08080.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTG | LOC_Os08g08080.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> GTGTG | LOC_Os08g08090.1 | upstream_gene_variant ; 4138.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> GTGTG | LOC_Os08g08084.1 | downstream_gene_variant ; 2466.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> GTGTG | LOC_Os08g08080.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> GTGTG | LOC_Os08g08080.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08090.1 | upstream_gene_variant ; 4133.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08084.1 | downstream_gene_variant ; 2461.0bp to feature; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08080.1 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| vg0804589533 | CTGTG -> CTGTGTGTGTGTGTGTGTGTGTGTGTGTG | LOC_Os08g08080.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.855; most accessible tissue: Callus, score: 82.924 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0804589533 | NA | 5.39E-07 | mr1693 | 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 |
| vg0804589533 | NA | 5.71E-10 | mr1567_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 |
| vg0804589533 | NA | 5.06E-06 | mr1567_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 |
| vg0804589533 | NA | 5.70E-08 | mr1612_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 |
| vg0804589533 | NA | 2.50E-06 | mr1720_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 |
| vg0804589533 | 2.57E-06 | 2.41E-06 | mr1721_2 | 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 |