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
122KP-S100P2A2selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
223KP-S100P2A3selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGACATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
324KP-S100P2A4selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
425KP-S100P2A5selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTCGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
521KP-S100P2A1selectionATGAGGATGTTATTGTGGTTTAGTGATGGCGTTGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
626KP-S100P2A6selectionATGAGGATGTTATTGTGGTTTAGTGATGGTGTTGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
729KP-S100P2A9selectionATGAGGATGTTATTGTGGTTTAGTGATGGTGTTGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
830KP-S100P2A10selectionATGAGGATGTTATTGTGGTTTAGTGATGGTGTTGAGATATAGGTGAATATTGTAAAATGTGGATGTTTGGAGGTAGTTTATATTTTGGGTTTTGGTTGGGGGAAAGGTTTTAGAAATGTTATTATAATGATGTATTTTATTAGAATTGAGTATATGAATGGGGAGGGGTAGGATTTTTTGAATGTTTTAATTTTATTGTTTTATTTTTTGTGTTAATATGAGGTTGTTTTATAAAGTATTAAGAGGTTGTTAGTGGGATATTTTTTTGGTTTTGTTAGTTTTTAGGAGGAAGGTG
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 [%] 62.5 50.0 0.0 0.0 0.0


CG site No.

62.5%50.0%0.0%0.0%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 77.5% (31 cases)
Methylated CpGs: 22.5% (9 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (40 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
22KP-S100P2A2selection 40.0
23KP-S100P2A3selection 40.0
24KP-S100P2A4selection 40.0
25KP-S100P2A5selection 40.0
21KP-S100P2A1selection 20.0
26KP-S100P2A6selection 0
29KP-S100P2A9selection 0
30KP-S100P2A10selection 0



Experiment Documentation

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