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
131KP-S100P3B1selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTCGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
232KP-S100P3B2selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTCGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
334KP-S100P3B4selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATGGTTATGGGTATGATTATAGACGTTTTTTTTCGGTATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
436KP-S100P3B6selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTCGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
540KP-S100P3B10selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGCTATGGGTATGATTATAGACGTTTTTTTTCGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
633KP-S100P3B3selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTT-GATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
735KP-S100P3B5selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTTGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
837KP-S100P3B7selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTTGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
939KP-S100P3B9selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTTGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
1038KP-S100P3B8selectionAGGAAGGTGGGTTTGAATTTAGTATCATGATGGAATTAGAGATAGTTATGGGTATGATTATAGACGTTTTTTTTTGATATTCGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
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 [%] 90.0 100.0 50.0 100.0 100.0 100.0


CG site No.

90.0%100.0%50.0%100.0%100.0%100.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 10.0% (6 cases)
Methylated CpGs: 90.0% (54 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (60 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
31KP-S100P3B1selection 100.0
32KP-S100P3B2selection 100.0
34KP-S100P3B4selection 100.0
36KP-S100P3B6selection 100.0
40KP-S100P3B10selection 100.0
33KP-S100P3B3selection 83.3
35KP-S100P3B5selection 83.3
37KP-S100P3B7selection 83.3
39KP-S100P3B9selection 83.3
38KP-S100P3B8selection 66.7



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/19/13
Project name RWPE1 Endpoint Comparison
Tissue B26
Gene or position S100P #3