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 GGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
180-Hyal12N5-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
288-Hyal12N13-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGGATTTTTAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
376-Hyal12N1-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
477-Hyal12N2-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGGTTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
578-Hyal12N3-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
679-Hyal12N4-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTACAAGATATGAAAGAATTTGGTTTTTAGTGTCATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGACAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
781-Hyal12N6-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTT--AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
882-Hyal12N7-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
983-Hyal12N8-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1084-Hyal12N9-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1185-Hyal12N10-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATGAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1286-Hyal12N11-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1387-Hyal12N12-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTCAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1490-Hyal12N15-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATCTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTCTGTTTTTGTTTATTTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
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 [%] 7.1 0.0 7.1 0.0 0.0 0.0 0.0


CG site No.

7.1%0.0%7.1%0.0%0.0%0.0%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 98.0% (96 cases)
Methylated CpGs: 2.0% (2 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (98 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
80-Hyal12N5-M13R.ab1selection 14.3
88-Hyal12N13-M13R.ab1selection 14.3
76-Hyal12N1-M13R.ab1selection 0
77-Hyal12N2-M13R.ab1selection 0
78-Hyal12N3-M13R.ab1selection 0
79-Hyal12N4-M13R.ab1selection 0
81-Hyal12N6-M13R.ab1selection 0
82-Hyal12N7-M13R.ab1selection 0
83-Hyal12N8-M13R.ab1selection 0
84-Hyal12N9-M13R.ab1selection 0
85-Hyal12N10-M13R.ab1selection 0
86-Hyal12N11-M13R.ab1selection 0
87-Hyal12N12-M13R.ab1selection 0
90-Hyal12N15-M13R.ab1selection 0



Experiment Documentation

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