Variant ID: vg1105183878 (JBrowse) | Variation Type: INDEL |
Chromosome: chr11 | Position: 5183878 |
Reference Allele: AGGGG | Alternative Allele: ACTCTGGCATGGGG,ACTCTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG,A |
Primary Allele: AGGGG | Secondary Allele: ACTCTGGGG |
Inferred Ancestral Allele: Not determined.
AGATTCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTT[AGGGG/ACTCTGGCATGGGG,ACTCTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG,A]
CTGTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCCA
TGGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAACAG[CCCCT/CCCCATGCCAGAGT,CCCCAGAGT,CCCCAAAGCTTAAGCTACTCATGCCAGAGT,CCCCACCAAAGCTTAAGCTACTCATGCCAGAGT,T]
AAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGAATCT
Populations | Population Size | Frequency of AGGGG(primary allele) | Frequency of ACTCTGGGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 9.90% | 5.80% | 30.83% | 44.60% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 4.55%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 3.24%; ACTCTGGCATGGGG: 0.61%; A: 0.42% |
All Indica | 2759 | 0.80% | 4.70% | 28.89% | 57.74% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 3.91%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 2.94%; ACTCTGGCATGGGG: 0.69%; A: 0.40% |
All Japonica | 1512 | 28.20% | 8.10% | 33.40% | 20.70% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 5.16%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 3.64%; ACTCTGGCATGGGG: 0.53%; A: 0.33% |
Aus | 269 | 0.70% | 7.10% | 37.92% | 40.15% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 8.92%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 3.72%; A: 1.12%; ACTCTGGCATGGGG: 0.37% |
Indica I | 595 | 1.80% | 1.30% | 17.82% | 76.47% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 1.34%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 0.67%; A: 0.50% |
Indica II | 465 | 0.40% | 1.30% | 11.40% | 84.30% | ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 0.86%; ACTCTGGCATGGGG: 0.86%; ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 0.65%; A: 0.22% |
Indica III | 913 | 0.20% | 9.10% | 41.40% | 36.47% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 6.24%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 4.60%; ACTCTGGCATGGGG: 1.42%; A: 0.55% |
Indica Intermediate | 786 | 0.80% | 4.10% | 33.08% | 52.54% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 5.09%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 3.94%; ACTCTGGCATGGGG: 0.25%; A: 0.25% |
Temperate Japonica | 767 | 33.60% | 6.00% | 30.25% | 23.34% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 3.52%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 2.61%; ACTCTGGCATGGGG: 0.39%; A: 0.26% |
Tropical Japonica | 504 | 14.10% | 12.30% | 38.89% | 18.65% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 9.33%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 5.16%; ACTCTGGCATGGGG: 0.99%; A: 0.60% |
Japonica Intermediate | 241 | 40.20% | 5.80% | 31.95% | 16.60% | ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 3.73%; ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 1.66% |
VI/Aromatic | 96 | 4.20% | 5.20% | 23.96% | 57.29% | ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 5.21%; ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 2.08%; A: 1.04%; ACTCTGGCATGGGG: 1.04% |
Intermediate | 90 | 17.80% | 0.00% | 33.33% | 43.33% | ACTCTGGCATGAGTAGCTTAAGCTTTGGGG: 3.33%; ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG: 2.22% |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1105183878 | AGGGG -> A | LOC_Os11g09710.1 | frameshift_variant ; p.Arg318fs; HIGH | frameshift_variant | Average:18.986; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
vg1105183878 | AGGGG -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:18.986; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
vg1105183878 | AGGGG -> ACTCTGGCATGAGTAGCTTAAGCTTTGGGG | LOC_Os11g09710.1 | frameshift_variant&stop_gained ; p.Arg318fs; HIGH | frameshift_variant | Average:18.986; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
vg1105183878 | AGGGG -> ACTCTGGCATGGGG | LOC_Os11g09710.1 | disruptive_inframe_insertion ; p.Arg318delinsThrLeuAlaTrp; MODERATE | inframe_variant | Average:18.986; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
vg1105183878 | AGGGG -> ACTCTGGCATGAGTAGCTTAAGCTTTGGTG GGG | LOC_Os11g09710.1 | frameshift_variant&stop_gained ; p.Arg318fs; HIGH | frameshift_variant | Average:18.986; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
vg1105183878 | AGGGG -> ACTCTGGGG | LOC_Os11g09710.1 | frameshift_variant ; p.Arg318fs; HIGH | frameshift_variant | Average:18.986; most accessible tissue: Callus, score: 53.099 | N | N | N | N |