Variant ID: vg0825541770 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 25541770 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCTGAGTACTTTTGGTTGTCGTTTGTAGGGATGTCGATGTCGAGGATGTCCAGCAGCGTGGGCAGCCCAAGTTACCGGTGGTCGCCCCGGCGATTACCCT[T/C]
CAAACGCCTATGTCGCAGGACGATATGGGACGAAACTCACCCGTGGAAATGGGCATGGCGATGACCTCCGTAGGTTGGTGATCTTTGTTTTCATCTCCTT
AAGGAGATGAAAACAAAGATCACCAACCTACGGAGGTCATCGCCATGCCCATTTCCACGGGTGAGTTTCGTCCCATATCGTCCTGCGACATAGGCGTTTG[A/G]
AGGGTAATCGCCGGGGCGACCACCGGTAACTTGGGCTGCCCACGCTGCTGGACATCCTCGACATCGACATCCCTACAAACGACAACCAAAAGTACTCAGG
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 84.50% | 2.00% | 6.47% | 7.02% | NA |
All Indica | 2759 | 74.60% | 3.30% | 10.76% | 11.38% | NA |
All Japonica | 1512 | 99.00% | 0.00% | 0.46% | 0.53% | NA |
Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
Indica I | 595 | 69.10% | 2.50% | 9.58% | 18.82% | NA |
Indica II | 465 | 48.00% | 7.10% | 18.71% | 26.24% | NA |
Indica III | 913 | 96.40% | 0.50% | 2.96% | 0.11% | NA |
Indica Intermediate | 786 | 69.10% | 4.80% | 16.03% | 10.05% | NA |
Temperate Japonica | 767 | 98.60% | 0.00% | 0.65% | 0.78% | NA |
Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.41% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 86.70% | 0.00% | 2.22% | 11.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0825541770 | T -> C | LOC_Os08g40340.1 | missense_variant ; p.Ser581Pro; MODERATE | nonsynonymous_codon ; S581P | Average:27.617; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 | unknown | unknown | TOLERATED | 0.16 |
vg0825541770 | T -> DEL | LOC_Os08g40340.1 | N | frameshift_variant | Average:27.617; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0825541770 | 2.14E-07 | 6.69E-06 | mr1913 | 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 |