| Variant ID: vg0130377630 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 30377630 |
| Reference Allele: GT | Alternative Allele: AT,G |
| Primary Allele: GT | Secondary Allele: AT |
Inferred Ancestral Allele: Not determined.
GTCATTAGCATATACGGGTTACTGTAACACTTATGGCTAATTATTAACTAATTAGGCTAAAAAGATTCGTCTCACGATTTTCCCCCTACCTGTGCAATTA[GT/AT,G]
TTTTTCTTTTAATCTATATTTAATGCTTTATGCATGTGTCCATATATTCGATGTAATATTTTTGAGAAAAAATTTTAGGGAACTAAGGCCTATAGTTTTC
GAAAACTATAGGCCTTAGTTCCCTAAAATTTTTTCTCAAAAATATTACATCGAATATATGGACACATGCATAAAGCATTAAATATAGATTAAAAGAAAAA[AC/AT,C]
TAATTGCACAGGTAGGGGGAAAATCGTGAGACGAATCTTTTTAGCCTAATTAGTTAATAATTAGCCATAAGTGTTACAGTAACCCGTATATGCTAATGAC
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.80% | 13.80% | 0.11% | 0.23% | G: 0.08% |
| All Indica | 2759 | 88.00% | 11.60% | 0.00% | 0.40% | G: 0.04% |
| All Japonica | 1512 | 80.20% | 19.50% | 0.26% | 0.00% | NA |
| Aus | 269 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 63.00% | 36.30% | 0.00% | 0.67% | NA |
| Indica II | 465 | 98.70% | 1.10% | 0.00% | 0.00% | G: 0.22% |
| Indica III | 913 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.30% | 8.80% | 0.00% | 0.89% | NA |
| Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 44.20% | 55.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 73.30% | 22.20% | 1.11% | 0.00% | G: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0130377630 | GT -> G | LOC_Os01g52790.1 | upstream_gene_variant ; 714.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> G | LOC_Os01g52810.1 | upstream_gene_variant ; 3468.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> G | LOC_Os01g52810.2 | upstream_gene_variant ; 3468.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> G | LOC_Os01g52810.3 | upstream_gene_variant ; 3468.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> G | LOC_Os01g52800.1 | downstream_gene_variant ; 554.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> G | LOC_Os01g52790-LOC_Os01g52800 | intergenic_region ; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> DEL | N | N | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> AT | LOC_Os01g52790.1 | upstream_gene_variant ; 713.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> AT | LOC_Os01g52810.1 | upstream_gene_variant ; 3469.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> AT | LOC_Os01g52810.2 | upstream_gene_variant ; 3469.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> AT | LOC_Os01g52810.3 | upstream_gene_variant ; 3469.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> AT | LOC_Os01g52800.1 | downstream_gene_variant ; 555.0bp to feature; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| vg0130377630 | GT -> AT | LOC_Os01g52790-LOC_Os01g52800 | intergenic_region ; MODIFIER | silent_mutation | Average:55.351; most accessible tissue: Minghui63 panicle, score: 68.46 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0130377630 | NA | 1.68E-10 | mr1539 | 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 |
| vg0130377630 | NA | 3.07E-08 | mr1676 | 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 |
| vg0130377630 | NA | 4.34E-07 | mr1785 | 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 |
| vg0130377630 | NA | 3.33E-06 | mr1807 | 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 |
| vg0130377630 | NA | 1.14E-07 | mr1398_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 |
| vg0130377630 | NA | 2.03E-07 | mr1401_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 |
| vg0130377630 | NA | 5.43E-07 | mr1551_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 |
| vg0130377630 | NA | 6.00E-06 | mr1606_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 |
| vg0130377630 | 1.48E-06 | 1.38E-10 | mr1676_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 |
| vg0130377630 | NA | 5.79E-06 | mr1682_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 |
| vg0130377630 | NA | 1.16E-09 | mr1916_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 |
| vg0130377630 | NA | 5.27E-07 | mr1991_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 |