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
101-Hyal12R1-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTT--T-AGGAGTTTTTGGTGTAG
202-Hyal12R2-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGGATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTGAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTT--AGGAGTTTTTGGTGTAG
303-Hyal12R3-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAGTTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTT--AGGAGTTTTTGGTGTAG
404-Hyal12R4-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTA-
505-Hyal12R5-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGGATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTT--T-AGGAGTTTTTGGTGTAG
606-Hyal12R6-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
707-Hyal12R7-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTT--AGGAGTTTTTGGTGTAG
809-Hyal12R9-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
911-Hyal12R11-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAGGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1013-Hyal12R13-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTTTAGGAGTTTTTGGTGTAG
1110-Hyal12R10-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTGGTAGGGTTTGTTTTTGTTTATTTTTTT-AGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTTGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-AGGAGTTTTTGGTG---
1214-Hyal12R14-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTCTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1308-Hyal12R8-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTACGTGGATAAAGAATATTTTTTGAGTATAAGATACGAAAGAATTCGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTTGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGTGGTTTTTTTTTTT-AGGAGTTTTTGGTGTAG
1415-Hyal12R15-M13R.ab1selectionGGGTTTATTAATGTTAGATGTAGTTATGTGGATAAAGAATATTTTTTGAGTATAAGATATGAAAGAATTTGGTTTTTAGTGTTATAAATAGGTTTGTTTAGTAGGGTTTGTTTTTGTTTATTTTTTTTAGTTTAGGTAAGGTTATAAAGTTTTGTTTTAGTGTTGATAGCGTGGGAGGGGTTATTGTTGGTTTAGTTTTATTTTTAATTAAGATTTTTTTGTTAGGGATTTAGAGGTAGTTTTGATGTTTGGTTGGTTTGGTTTTTTAATTTAAGGTTCGTTTTTTGGTTCGTTTTTGGTTTGGGTGGGGTGATTTTTTATAAAAGTTTAGAATTTTTAGTAGCGGTTTTTTTTTTT-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 [%] 92.9 92.9 92.9 100.0 92.9 92.9 85.7


CG site No.

92.9%92.9%92.9%100.0%92.9%92.9%85.7%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 7.1% (7 cases)
Methylated CpGs: 92.9% (91 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 
01-Hyal12R1-M13R.ab1selection 100.0
02-Hyal12R2-M13R.ab1selection 100.0
03-Hyal12R3-M13R.ab1selection 100.0
04-Hyal12R4-M13R.ab1selection 100.0
05-Hyal12R5-M13R.ab1selection 100.0
06-Hyal12R6-M13R.ab1selection 100.0
07-Hyal12R7-M13R.ab1selection 100.0
09-Hyal12R9-M13R.ab1selection 100.0
11-Hyal12R11-M13R.ab1selection 100.0
13-Hyal12R13-M13R.ab1selection 100.0
10-Hyal12R10-M13R.ab1selection 85.7
14-Hyal12R14-M13R.ab1selection 85.7
08-Hyal12R8-M13R.ab1selection 71.4
15-Hyal12R15-M13R.ab1selection 57.1



Experiment Documentation

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