BISMA results:

Reference sequence (original) : CTTCCCAAAGTGCTAGGATTATAGGCGTGAGCCTCCGCACCTGGCATGCCTGGCCATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATCCACGAAAGTAAAGTGCCTAGGGCCCATCAATGTCAGATGCAGCCACGTGGACAAAGAACACTCCCTGAGCA
Reference sequence (converted): TTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
Number CpG in Reference sequence: 4

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     
                   2                   4                   6                   8                   0                   2                   4                   6     
Number Sequence_id                    0                   0                   0                   0                   0                   0                   0                   0     
Reference TTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
162KP-Hyal11A1selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
263KP-Hyal11A2selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
364KP-Hyal11A3selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
467KP-Hyal11A6selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
568KP-Hyal11A7selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
669KP-Hyal11A8selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
771KP-Hyal11A10selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
870KP-Hyal11A9selectionTTTTTTAAAGTGTTAGGATTATAGGTGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
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
CpG position 26 36 94 137
Methylation [%] 87.5 100.0 100.0 0.0


CG site No.

87.5%100.0%100.0%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 28.1% (9 cases)
Methylated CpGs: 71.9% (23 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (32 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
62KP-Hyal11A1selection 75.0
63KP-Hyal11A2selection 75.0
64KP-Hyal11A3selection 75.0
67KP-Hyal11A6selection 75.0
68KP-Hyal11A7selection 75.0
69KP-Hyal11A8selection 75.0
71KP-Hyal11A10selection 75.0
70KP-Hyal11A9selection 50.0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/19/13
Project name RWPE1 Endpoint Comparison
Tissue CAsE-PE
Gene or position Hyal1 #1