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
112KP-Aldh1a11C2selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTCGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
219KP-Aldh1a11C9selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTCGAGTATGTAAATAAATTTTAGTTTGTGTAGATGAAAAAGGAATAAATAAAGTTAAGTGT
315KP-Aldh1a11C5selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTCGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
413KP-Aldh1a11C3selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
516KP-Aldh1a11C6selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTNGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
617KP-Aldh1a11C7selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTT--TGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT
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 [%] 33.3 0.0 0.0 0.0 40.0 16.7


CG site No.

33.3%0.0%0.0%0.0%40.0%16.7%
Using scale :




Methylation statistics:

Average methylation over all sequences:

DNA methylation summary over all sequences
Unmethylated CpGs: 85.7% (30 cases)
Methylated CpGs: 14.3% (5 cases)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 97.2% (35 cases)
CpGs not analyzed: 2.8% (1 case)


Average methylation for each clone:

Seq. identifier Average 
12KP-Aldh1a11C2selection 33.3
19KP-Aldh1a11C9selection 33.3
15KP-Aldh1a11C5selection 16.7
13KP-Aldh1a11C3selection 0
16KP-Aldh1a11C6selection 0
17KP-Aldh1a11C7selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 9/20/13
Project name RWPE1 Endpoint Comparison
Tissue CTPE
Gene or position Aldh1a1 #1