BISMA results:

Reference sequence (original) : ATGAGGATGCCACTGTGGCTCAGTGATGGCGCCGAGACACAGGTGAACACTGTAAAATGTGGATGCCTGGAGGCAGCCCACACCCTGGGCCTTGGCTGGGGGAAAGGTTCCAGAAACGTCATCACAACGATGCATTTCATCAGAACTGAGCACATGAATGGGGAGGGGCAGGACTTCCTGAATGTCCCAACCCCACTGTCCCACCCTCTGTGTCAATATGAGGCTGCCTTATAAAGCACCAAGAGGCTGCCAGTGGGACATTTTCTCGGCCCTGCCAGCCCCCAGGAGGAAGGTG
Reference sequence (converted): ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTCGGTTTTGTTAGTTTTTAGGAGGAAGGTG
Number CpG in Reference sequence: 5

Parameters used:

Alignment mode: pairwise alignment of reference sequence and experimental sequences
Lower threshold conversion rate: 95%
Lower threshold sequence identity: 90%
Upper threshold of N-sites at cytosine positions: 20%
Upper threshold insertions/deletions: 20%

Final sequence alignment of the sequences included:

                                                                                                                                                                                                                                                                                                          
                                                                                                   1                   1                   1                   1                   1                   2                   2                   2                   2                   2                  
                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                   6                   8                  
Number Sequence_id                    0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                  
Reference ATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTCGGTTTTGTTAGTTTTTAGGAGGAAGGTG
151KP-S100P2N1selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTATAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
253KP-S100P2N3selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTTGAGATATAGGTGAATATTATAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAACGTTATTATAACGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
354KP-S100P2N4selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
455KP-S100P2N5selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTATAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
556KP-S100P2N6selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
657KP-S100P2N7selectionATGAGGATGTTATTGTGGTTTAGTGATGGTGTTGAGGTATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
759KP-S100P2N9selectionATGAGGATGTTATTGTGGTTTAGTGATGGTGTTGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
Legend: methylated CpG position unmethylated CpG position unconverted cytosine cytosine at unexpected position

Methylation pattern in subclones:

methylated  , unmethylated  , unknown 

Methylation status of CpG-sites cytosine in the sequence context


Methylation pattern



Average methylation for each CpG site:

CpG site 1 2 3 4 5
CpG position 30 33 117 128 267
Methylation [%] 71.4 57.1 14.3 28.6 0.0


CG site No.

71.4%57.1%14.3%28.6%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 65.7% (23 cases)
Methylated CpGs: 34.3% (12 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (35 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
51KP-S100P2N1selection 60.0
53KP-S100P2N3selection 60.0
54KP-S100P2N4selection 40.0
55KP-S100P2N5selection 40.0
56KP-S100P2N6selection 40.0
57KP-S100P2N7selection 0
59KP-S100P2N9selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 8/26/13
Project name RWPE1 Endpoint Comparison
Organism human
Tissue negative control
Gene or position S100P #2