BISMA results:

Reference sequence (original) : TGGCCTTAGTGGCCAGAGCAGCTGCTGCATACACTTATCACAGGTTTCGGCTTTGTAAATTAATTCATCTGCAAATAGTGCACTGTCTCCAGGTACAAATTCGATGCTGGAGCACTGGTTTCTTAAGGATTTAAGTTTAAAGTCAAAGGCTTCCTGCCCTAGGTGTTACAAATAAGTAGTGTCGTTTTCTTTTTTTGCTCTGAGTTTGTTCATCCAATCGTATCCGAGTATGCAAATAAACTTTAGCCCGTGCAGATAAAAAAGGAACAAATAAAGCCAAGTGC
Reference sequence (converted): TGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTCGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTCGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATCGTATTCGAGTATGTAAATAAATTTTAGTTCGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
Number CpG in Reference sequence: 6

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       
                   2                   4                   6                   8                   0                   2                   4                   6                   8                   0                   2                   4                   6                   8       
Number Sequence_id                    0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0                   0       
Reference TGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTCGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTCGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATCGTATTCGAGTATGTAAATAAATTTTAGTTCGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
124KP-Aldh1a11A4selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATCGTATTCGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
227KP-Aldh1a11A7selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTCGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
329KP-Aldh1a11A9selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGCATATACTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTCGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
422KP-Aldh1a11A2selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGCTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
525KP-Aldh1a11A5selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
626KP-Aldh1a11A6selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
728KP-Aldh1a11A8selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
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
CpG position 48 102 183 219 225 249
Methylation [%] 0.0 0.0 0.0 14.3 42.9 0.0


CG site No.

0.0%0.0%0.0%14.3%42.9%0.0%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 90.5% (38 cases)
Methylated CpGs: 9.5% (4 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (42 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
24KP-Aldh1a11A4selection 33.3
27KP-Aldh1a11A7selection 16.7
29KP-Aldh1a11A9selection 16.7
22KP-Aldh1a11A2selection 0
25KP-Aldh1a11A5selection 0
26KP-Aldh1a11A6selection 0
28KP-Aldh1a11A8selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/20/13
Project name RWPE1 Endpoint Comparison
Sex CAsE-PE