BISMA results:

Reference sequence (original) : GGGCCCATCAATGTCAGATGCAGCCACGTGGACAAAGAACACTCCCTGAGCACAAGACACGAAAGAACCCGGTCTCCAGTGTCACAAACAGGCCTGCCCAGCAGGGTCTGCCCCTGCCCACCTCCTCCAGCCTAGGTAAGGCCACAAAGCCCTGCCCTAGTGCTGACAGCGTGGGAGGGGCCACTGTTGGCCCAGCCCCACCCCCAACCAAGATCCCTTTGCCAGGGATTCAGAGGTAGCCCTGATGCCTGGCTGGCCTGGCCTCCTAATCCAAGGCCCGCCCCTTGGCCCGCCCCTGGCCTGGGTGGGGTGACCCCCTACAAAAGCTCAGAATTTCCAGCAGCGGCTCCTTCCTCCAGGAGTCTCTGGTGCAG
Reference sequence (converted): GGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
Number CpG in Reference sequence: 7

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                   1                   2                   2                   2                   2                   2                   3                   3                   3                    3                 
                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                    6                 
Number Sequence_id                    0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                    0                 
Reference GGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
146-Hyal12B1-M13R.ab1selectionGGGTTTATTAATGTNANATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
247-Hyal12B2-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAGTAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGCTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTCTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTT--AGGAGTTTTTGGTGTAG
348-Hyal12B3-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTTAGGAGTTTTTGGTGTAG
449-Hyal12B4-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTT--AGGAGTTTTTGGTGTAG
551-Hyal12B6-M13R.ab1selection-GGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGACACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGCTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTT--T-AGGAGTTTTTGGTGTAG
652-Hyal12B7-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTGTAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAACAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTTAGGAGTTTTTGGTGTAG
753-Hyal12B8-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
854-Hyal12B9-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
955-Hyal12B10-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTCTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATCTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1056-Hyal12B11-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1158-Hyal12B13-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGCGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1259-Hyal12B14-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1350-Hyal12B5-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTT--AGGAGTTTTTGGTGTAG
1457-Hyal12B12-M13R.ab1selection-GGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTCATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1560-Hyal12B15-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTCATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTT--AGGAGTTTTTGGTGTAG
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 7
CpG position 27 60 70 170 279 291 344
Methylation [%] 100.0 93.3 93.3 100.0 100.0 93.3 100.0


CG site No.

100.0%93.3%93.3%100.0%100.0%93.3%100.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 2.9% (3 cases)
Methylated CpGs: 97.1% (102 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (105 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
46-Hyal12B1-M13R.ab1selection 100.0
47-Hyal12B2-M13R.ab1selection 100.0
48-Hyal12B3-M13R.ab1selection 100.0
49-Hyal12B4-M13R.ab1selection 100.0
51-Hyal12B6-M13R.ab1selection 100.0
52-Hyal12B7-M13R.ab1selection 100.0
53-Hyal12B8-M13R.ab1selection 100.0
54-Hyal12B9-M13R.ab1selection 100.0
55-Hyal12B10-M13R.ab1selection 100.0
56-Hyal12B11-M13R.ab1selection 100.0
58-Hyal12B13-M13R.ab1selection 100.0
59-Hyal12B14-M13R.ab1selection 100.0
50-Hyal12B5-M13R.ab1selection 85.7
57-Hyal12B12-M13R.ab1selection 85.7
60-Hyal12B15-M13R.ab1selection 85.7



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 1/16/14
Project name RWPE1 Endpoint Comparison
Tissue B26
Gene or position Hyal1 #2