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
123KP-S100P3A3selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
225KP-S100P3A5selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
326KP-S100P3A6selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTCGATATTTGGGTAGCGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
430KP-S100P3A10selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGCGAGGGTAGTACGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
522KP-S100P3A2selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
627KP-S100P3A7selectionAGGAAGGTGGGTTTGAATTTAGTATTATGACGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
724KP-S100P3A4selectionAGGAAGGTGGGTTTGAATTTAGTATTATGATGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTT-GATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
828KP-S100P3A8selectionAGGAAGGTGGGTTTGAATTTAGTATTATGATGGAATTAGAGATAGTTATGGGTATGATTATAGATGTTTTTTTTTGATATTTGGGTAGTGAGGGTAGTATGTAGATTTTGATTAAGGGGGAGTTTAAGGTGTTGATGGAGAAGGAGTTATTAGG
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 [%] 75.0 0.0 12.5 0.0 50.0 37.5


CG site No.

75.0%0.0%12.5%0.0%50.0%37.5%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 70.8% (34 cases)
Methylated CpGs: 29.2% (14 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (48 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
23KP-S100P3A3selection 50.0
25KP-S100P3A5selection 50.0
26KP-S100P3A6selection 50.0
30KP-S100P3A10selection 50.0
22KP-S100P3A2selection 16.7
27KP-S100P3A7selection 16.7
24KP-S100P3A4selection 0
28KP-S100P3A8selection 0



Experiment Documentation

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