| Variant ID: vg1121157956 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21157956 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.01, others allele: 0.00, population size: 268. )
TTTGAGTCATTGCTCACCAAACAAATTGCGGAAATTATATTTGTCCAACAACAATATTACGGGAACTCTACCAGCTCAGAGTATGGGCCAATTTACCAGC[T/A]
TAGCCAATATTGGTTTCTCTTTCAACCAGCTCACAGGGCACGTGCCTCCTGAGATTGGTAAACTAGCTAGTTTGACTCACCTTGACCTAAGTGAAAATAA
TTATTTTCACTTAGGTCAAGGTGAGTCAAACTAGCTAGTTTACCAATCTCAGGAGGCACGTGCCCTGTGAGCTGGTTGAAAGAGAAACCAATATTGGCTA[A/T]
GCTGGTAAATTGGCCCATACTCTGAGCTGGTAGAGTTCCCGTAATATTGTTGTTGGACAAATATAATTTCCGCAATTTGTTTGGTGAGCAATGACTCAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.70% | 9.70% | 1.76% | 8.80% | NA |
| All Indica | 2759 | 84.00% | 1.00% | 1.41% | 13.56% | NA |
| All Japonica | 1512 | 69.20% | 27.60% | 2.45% | 0.73% | NA |
| Aus | 269 | 91.40% | 0.00% | 0.37% | 8.18% | NA |
| Indica I | 595 | 96.60% | 0.00% | 1.01% | 2.35% | NA |
| Indica II | 465 | 77.60% | 0.60% | 2.58% | 19.14% | NA |
| Indica III | 913 | 80.00% | 2.00% | 0.66% | 17.42% | NA |
| Indica Intermediate | 786 | 83.00% | 0.90% | 1.91% | 14.25% | NA |
| Temperate Japonica | 767 | 90.60% | 6.00% | 2.48% | 0.91% | NA |
| Tropical Japonica | 504 | 36.30% | 60.70% | 2.58% | 0.40% | NA |
| Japonica Intermediate | 241 | 69.70% | 27.40% | 2.07% | 0.83% | NA |
| VI/Aromatic | 96 | 93.80% | 3.10% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 75.60% | 11.10% | 6.67% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121157956 | T -> A | LOC_Os11g36000.1 | missense_variant ; p.Leu334Ile; MODERATE | nonsynonymous_codon ; L334I | Average:49.108; most accessible tissue: Callus, score: 84.645 | unknown | unknown | TOLERATED | 0.05 |
| vg1121157956 | T -> DEL | LOC_Os11g36000.1 | N | frameshift_variant | Average:49.108; most accessible tissue: Callus, score: 84.645 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121157956 | NA | 4.17E-06 | mr1502 | 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 |
| vg1121157956 | NA | 9.43E-06 | mr1502 | 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 |
| vg1121157956 | NA | 5.24E-06 | mr1543 | 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 |
| vg1121157956 | NA | 5.78E-09 | mr1648 | 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 |
| vg1121157956 | NA | 7.96E-13 | mr1871 | 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 |
| vg1121157956 | NA | 6.19E-12 | mr1398_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 |
| vg1121157956 | NA | 1.86E-08 | mr1398_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 |
| vg1121157956 | NA | 3.34E-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 |
| vg1121157956 | NA | 2.55E-07 | mr1696_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 |
| vg1121157956 | NA | 2.30E-09 | mr1705_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 |
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