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
112KP-S100P3C2selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGANGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
211KP-S100P3C1selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
313KP-S100P3C3selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
414KP-S100P3C4selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTCGATATTTGGGTAGTGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
516KP-S100P3C6selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
617KP-S100P3C7selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
720KP-S100P3C10selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGGTATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
815KP-S100P3C5selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTNGGGTAGCGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
918KP-S100P3C8selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGANGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
1019KP-S100P3C9selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
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 0.0 10.0 0.0 70.0 70.0


CG site No.

100.0%0.0%10.0%0.0%70.0%70.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 56.1% (32 cases)
Methylated CpGs: 43.9% (25 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 95.0% (57 cases)
CpGs not analyzed: 5.0% (3 cases)


Average methylation for each clone:

Seq. identifier Average 
12KP-S100P3C2selection 60.0
11KP-S100P3C1selection 50.0
13KP-S100P3C3selection 50.0
14KP-S100P3C4selection 50.0
16KP-S100P3C6selection 50.0
17KP-S100P3C7selection 50.0
20KP-S100P3C10selection 50.0
15KP-S100P3C5selection 40.0
18KP-S100P3C8selection 20.0
19KP-S100P3C9selection 16.7



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/19/13
Project name RWPE1 Endpoint Comparison