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
136KP-S100P2B6selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTCGGTTTTGTTAGTTTTTAGGAGGAAGGTG
240KP-S100P2B10selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTCGGTTTTGTTAGTTTTTAGGAGGAAGGTG
331KP-S100P2B1selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
432KP-S100P2B2selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
533KP-S100P2B3selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
634KP-S100P2B4selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
735KP-S100P2B5selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGCTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
837KP-S100P2B7selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGCTTTGTTAGTTTTT-GGAGGAAGGTG
938KP-S100P2B8selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTCATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
1039KP-S100P2B9selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTCTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
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 [%] 100.0 100.0 0.0 0.0 20.0


CG site No.

100.0%100.0%0.0%0.0%20.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 56.0% (28 cases)
Methylated CpGs: 44.0% (22 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (50 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
36KP-S100P2B6selection 60.0
40KP-S100P2B10selection 60.0
31KP-S100P2B1selection 40.0
32KP-S100P2B2selection 40.0
33KP-S100P2B3selection 40.0
34KP-S100P2B4selection 40.0
35KP-S100P2B5selection 40.0
37KP-S100P2B7selection 40.0
38KP-S100P2B8selection 40.0
39KP-S100P2B9selection 40.0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/18/13
Project name RWPE1 Endpoint Comparison
Tissue B26
Gene or position S100P #2