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
124KP-Hyal11B9bselectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
272KP-Hyal11B1selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
374KP-Hyal11B3selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
475KP-Hyal11B4selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTACTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
576KP-Hyal11B5selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
677KP-Hyal11B6selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
778KP-Hyal11B7selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
879KP-Hyal11B8selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTA
973KP-Hyal11B2selectionTTTTTTAAAGTGTTAGGATTATAGGCGTGAGTTTTCGTATTTGGTATGTTTGGTTATATTTTAAAATATTTTTTTTAAGGAGGAAAAGATTTACGAAAGTAAAGTGTTTAGGGTTTATTGATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTA
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 88.9


CG site No.

100.0%100.0%100.0%88.9%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 2.8% (1 case)
Methylated CpGs: 97.2% (35 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (36 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
24KP-Hyal11B9bselection 100.0
72KP-Hyal11B1selection 100.0
74KP-Hyal11B3selection 100.0
75KP-Hyal11B4selection 100.0
76KP-Hyal11B5selection 100.0
77KP-Hyal11B6selection 100.0
78KP-Hyal11B7selection 100.0
79KP-Hyal11B8selection 100.0
73KP-Hyal11B2selection 75.0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 10/21/13
Project name RWPE1 Endpoint Comparison
Tissue B26
Gene or position Hyal1 #1