| Variant ID: vg1001981255 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1981255 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTTAGATTTGATCTTAGAGAACGATTCTTTCGGCCGAAGCGAAGCCGTCCCGGAGGTCAAGATTATTTATGAAGATCCTCTGCACGAGGAGTTGGAACCC[A/G]
ACTCAACTGCCGAATCCTCATTCCGGTTGCTGGAGCCAGAGGAAGAGGAAATTCATCCTCCAGAAATTCCATTCCAATTCAAGGATGATCTTTATGAAGA
TCTTCATAAAGATCATCCTTGAATTGGAATGGAATTTCTGGAGGATGAATTTCCTCTTCCTCTGGCTCCAGCAACCGGAATGAGGATTCGGCAGTTGAGT[T/C]
GGGTTCCAACTCCTCGTGCAGAGGATCTTCATAAATAATCTTGACCTCCGGGACGGCTTCGCTTCGGCCGAAAGAATCGTTCTCTAAGATCAAATCTAAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.00% | 14.70% | 0.78% | 11.45% | NA |
| All Indica | 2759 | 75.30% | 7.90% | 0.94% | 15.91% | NA |
| All Japonica | 1512 | 70.00% | 29.20% | 0.26% | 0.60% | NA |
| Aus | 269 | 58.00% | 7.80% | 1.49% | 32.71% | NA |
| Indica I | 595 | 60.20% | 22.20% | 1.34% | 16.30% | NA |
| Indica II | 465 | 81.30% | 6.20% | 0.86% | 11.61% | NA |
| Indica III | 913 | 78.10% | 0.80% | 0.44% | 20.70% | NA |
| Indica Intermediate | 786 | 79.90% | 6.20% | 1.27% | 12.60% | NA |
| Temperate Japonica | 767 | 57.00% | 42.20% | 0.13% | 0.65% | NA |
| Tropical Japonica | 504 | 95.40% | 4.40% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 58.10% | 39.40% | 1.24% | 1.24% | NA |
| VI/Aromatic | 96 | 94.80% | 3.10% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 76.70% | 16.70% | 2.22% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001981255 | A -> G | LOC_Os10g04250.1 | missense_variant ; p.Asn234Asp; MODERATE | nonsynonymous_codon | Average:23.26; most accessible tissue: Minghui63 flag leaf, score: 35.832 | unknown | unknown | TOLERATED | 1.00 |
| vg1001981255 | A -> DEL | LOC_Os10g04250.1 | N | frameshift_variant | Average:23.26; most accessible tissue: Minghui63 flag leaf, score: 35.832 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001981255 | 7.34E-07 | NA | mr1679 | 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 |
| vg1001981255 | NA | 5.04E-09 | mr1691 | 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 |
| vg1001981255 | NA | 3.42E-06 | mr1691 | 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 |
| vg1001981255 | NA | 3.77E-09 | mr1693 | 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 |
| vg1001981255 | NA | 2.28E-06 | mr1748 | 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 |
| vg1001981255 | NA | 4.45E-07 | mr1768 | 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 |
| vg1001981255 | NA | 5.89E-06 | mr1768_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 |