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
181KP-Hyal11P1selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
282KP-Hyal11P2selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTACGGTTTATTAATGTTAGATGTAGTTACGTGAATAAAGAATATTTTTAGAGTA
383KP-Hyal11P3selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTCAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
485KP-Hyal11P5selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
586KP-Hyal11P6selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
687KP-Hyal11P7selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
788KP-Hyal11P8selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
890KP-Hyal11P10selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTT-AAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
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 [%] 100.0 100.0 100.0 100.0


CG site No.

100.0%100.0%100.0%100.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 0.0% (0 case)
Methylated CpGs: 100.0% (32 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 
81KP-Hyal11P1selection 100.0
82KP-Hyal11P2selection 100.0
83KP-Hyal11P3selection 100.0
85KP-Hyal11P5selection 100.0
86KP-Hyal11P6selection 100.0
87KP-Hyal11P7selection 100.0
88KP-Hyal11P8selection 100.0
90KP-Hyal11P10selection 100.0



Experiment Documentation

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