BISMA results:

Reference sequence (original) : AGGAAGGTGGGTCTGAATCTAGCACCATGACGGAACTAGAGACAGCCATGGGCATGATCATAGACGTCTTTTCCCGATATTCGGGCAGCGAGGGCAGCACGCAGACCCTGACCAAGGGGGAGCTCAAGGTGCTGATGGAGAAGGAGCTACCAGG
Reference sequence (converted): AGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTCGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
Number CpG in Reference sequence: 6

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                 
                   2                   4                   6                   8                   0                   2                   4                 
Number Sequence_id                    0                   0                   0                   0                   0                   0                   0                 
Reference AGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTCGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
158KP-S100P3N8selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTTGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
252KP-S100P3N2selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
353KP-S100P3N3selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTACGCAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
460KP-S100P3N10selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTACGCAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
551KP-S100P3N1selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTANGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
654KP-S100P3N4selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
757KP-S100P3N7selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
859KP-S100P3N9selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTT-GATATTTGGGTAGTGAGGGCAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
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 6
CpG position 31 65 75 82 89 100
Methylation [%] 100.0 12.5 0.0 12.5 25.0 57.1


CG site No.

100.0%12.5%0.0%12.5%25.0%57.1%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 66.0% (31 cases)
Methylated CpGs: 34.0% (16 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 97.9% (47 cases)
CpGs not analyzed: 2.1% (1 case)


Average methylation for each clone:

Seq. identifier Average 
58KP-S100P3N8selection 83.3
52KP-S100P3N2selection 50.0
53KP-S100P3N3selection 33.3
60KP-S100P3N10selection 33.3
51KP-S100P3N1selection 20.0
54KP-S100P3N4selection 16.7
57KP-S100P3N7selection 16.7
59KP-S100P3N9selection 16.7



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/19/13
Project name RWPE1 Endpoint Comparison
Tissue negative control
Gene or position S100P #3