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 GGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
132-Hyal12A2-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTCTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
238-Hyal12A8-M13R.ab1selection-GGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGCAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGCGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
340-Hyal12A10-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTT--TAGGAGTTTTTGGTGTAG
443-Hyal12A13-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAGGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
531-Hyal12A1-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGCTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
633-Hyal12A3-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTGTAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
734-Hyal12A4-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
835-Hyal12A5-M13R.ab1selection-GGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTCTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTT--TAGGAGTTTTTGGTGTAG
936-Hyal12A6-M13R.ab1selection-GGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1037-Hyal12A7-M13R.ab1selection-GGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAGTAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAGGATTTCTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1139-Hyal12A9-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1241-Hyal12A11-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTCAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGCAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1342-Hyal12A12-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTCAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1444-Hyal12A14-M13R.ab1selectionGGGTTTATTAATGTTNNNTGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1545-Hyal12A15-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGTGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTTAGGAGTTTTTGGTGTAG
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 [%] 0.0 26.7 20.0 6.7 0.0 0.0 0.0


CG site No.

0.0%26.7%20.0%6.7%0.0%0.0%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 92.4% (97 cases)
Methylated CpGs: 7.6% (8 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 
32-Hyal12A2-M13R.ab1selection 28.6
38-Hyal12A8-M13R.ab1selection 28.6
40-Hyal12A10-M13R.ab1selection 28.6
43-Hyal12A13-M13R.ab1selection 28.6
31-Hyal12A1-M13R.ab1selection 0
33-Hyal12A3-M13R.ab1selection 0
34-Hyal12A4-M13R.ab1selection 0
35-Hyal12A5-M13R.ab1selection 0
36-Hyal12A6-M13R.ab1selection 0
37-Hyal12A7-M13R.ab1selection 0
39-Hyal12A9-M13R.ab1selection 0
41-Hyal12A11-M13R.ab1selection 0
42-Hyal12A12-M13R.ab1selection 0
44-Hyal12A14-M13R.ab1selection 0
45-Hyal12A15-M13R.ab1selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 1/16/14
Project name RWPE1 Endpoint Comparison
Tissue CAsE-PE
Gene or position Hayl1 #2