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Detailed information for vg1105183878:

Variant ID: vg1105183878 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 5183878
Reference Allele: AGGGGAlternative Allele: ACTCTGGCATGGGG,ACTCTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG,A
Primary Allele: AGGGGSecondary Allele: ACTCTGGGG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATTCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTT[AGGGG/ACTCTGGCATGGGG,ACTCTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGGG,ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG,A]
CTGTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCCA

Reverse complement sequence

TGGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAACAG[CCCCT/CCCCATGCCAGAGT,CCCCAGAGT,CCCCAAAGCTTAAGCTACTCATGCCAGAGT,CCCCACCAAAGCTTAAGCTACTCATGCCAGAGT,T]
AAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGAATCT

Allele Frequencies:

Populations Population SizeFrequency 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%

Allele Effect:

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