| Variant ID: vg0112635655 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 12635655 |
| Reference Allele: A | Alternative Allele: T,ATTT,ATT,AT |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, T: 0.08, others allele: 0.00, population size: 63. )
TCTAGATAAGTGTTCCATATTTTCATTAGAAATTTCCATACTTTTAGGTTTATCAGTCCCTCAACAGGATATTCGCTGATTCCTTCGGCCGAAAAATTCA[A/T,ATTT,ATT,AT]
TTTTTTTTCATTTAGCAAAATTTCCCCCAAAAATTTCCAAAACTCCAGCAATTCCAGTTACATCAATCCCCCATAAATGTTTTTTATTTCCATGATACTG
CAGTATCATGGAAATAAAAAACATTTATGGGGGATTGATGTAACTGGAATTGCTGGAGTTTTGGAAATTTTTGGGGGAAATTTTGCTAAATGAAAAAAAA[T/A,AAAT,AAT,AT]
TGAATTTTTCGGCCGAAGGAATCAGCGAATATCCTGTTGAGGGACTGATAAACCTAAAAGTATGGAAATTTCTAATGAAAATATGGAACACTTATCTAGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.40% | 21.10% | 0.32% | 44.31% | ATTT: 2.75%; ATT: 0.08%; AT: 0.02% |
| All Indica | 2759 | 4.20% | 19.70% | 0.51% | 71.33% | ATTT: 4.20%; ATT: 0.04% |
| All Japonica | 1512 | 83.80% | 13.20% | 0.07% | 2.71% | ATTT: 0.20% |
| Aus | 269 | 0.70% | 81.00% | 0.00% | 14.87% | ATTT: 2.97%; AT: 0.37% |
| Indica I | 595 | 4.40% | 4.40% | 0.84% | 90.25% | ATTT: 0.17% |
| Indica II | 465 | 4.50% | 46.90% | 0.65% | 44.95% | ATTT: 3.01% |
| Indica III | 913 | 3.90% | 11.20% | 0.22% | 77.11% | ATTT: 7.56% |
| Indica Intermediate | 786 | 4.20% | 25.20% | 0.51% | 65.90% | ATTT: 4.07%; ATT: 0.13% |
| Temperate Japonica | 767 | 93.00% | 6.00% | 0.13% | 0.91% | NA |
| Tropical Japonica | 504 | 71.60% | 21.80% | 0.00% | 5.95% | ATTT: 0.60% |
| Japonica Intermediate | 241 | 80.10% | 18.30% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 62.50% | 11.50% | 0.00% | 26.04% | NA |
| Intermediate | 90 | 45.60% | 25.60% | 0.00% | 22.22% | ATTT: 3.33%; ATT: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112635655 | A -> AT | LOC_Os01g22480.1 | downstream_gene_variant ; 787.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> AT | LOC_Os01g22480.2 | downstream_gene_variant ; 724.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> AT | LOC_Os01g22450-LOC_Os01g22480 | intergenic_region ; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> T | LOC_Os01g22480.1 | downstream_gene_variant ; 788.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> T | LOC_Os01g22480.2 | downstream_gene_variant ; 725.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> T | LOC_Os01g22450-LOC_Os01g22480 | intergenic_region ; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> ATT | LOC_Os01g22480.1 | downstream_gene_variant ; 787.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> ATT | LOC_Os01g22480.2 | downstream_gene_variant ; 724.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> ATT | LOC_Os01g22450-LOC_Os01g22480 | intergenic_region ; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> ATTT | LOC_Os01g22480.1 | downstream_gene_variant ; 787.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> ATTT | LOC_Os01g22480.2 | downstream_gene_variant ; 724.0bp to feature; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> ATTT | LOC_Os01g22450-LOC_Os01g22480 | intergenic_region ; MODIFIER | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0112635655 | A -> DEL | N | N | silent_mutation | Average:35.244; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0112635655 | NA | 3.25E-06 | mr1333 | 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 |
| vg0112635655 | NA | 6.00E-06 | mr1457_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 |
| vg0112635655 | NA | 8.65E-06 | mr1961_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 |