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
		

		
103KP-Aldh1a11R5bselectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTCGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGCATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT

		
201KP-Aldh1a11R1selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTACTGTTTTTAGGTATAAATTTGATGTTGGAGTATCGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTCTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTT--TGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT

		
302KP-Aldh1a11R2selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT

		
405KP-Aldh1a11R8bselection---GTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTT-GTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT

		
510KP-Aldh1a11R10selectionTGGTTTTAGTGGTTAGAGTAGTTGTTGTATATATTTATTATAGGTTTTGGTTTTGTAAATTAATTTATTTGTAAATAGTGTATTGTTTTTAGGTATAAATTTGATGTTGGAGTATTGGTTTTTTAAGGATTTAAGTTTAAAGTTAAAGGTTTTTTGTTTTAGGTGTTATAAATAAGTAGTGTTGTTTTTTTTTTTTGTTTTGAGTTTGTTTATTTAATTGTATTTGAGTATGTAAATAAATTTTAGTTTGTGTAGATAAAAAAGGAATAAATAAAGTTAAGTGT

	

	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 [%] 20.0 0.0 0.0 0.0 0.0 0.0


CG site No.

20.0%0.0%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: 96.7% (29 cases)
Methylated CpGs: 3.3% (1 case)
Statistics about CpGs analyzed over all sequences
CpGs analyzed: 100.0% (30 cases)
CpGs not analyzed: 0.0% (0 case)


Average methylation for each clone:

Seq. identifier Average 
03KP-Aldh1a11R5bselection 16.7
01KP-Aldh1a11R1selection 0
02KP-Aldh1a11R2selection 0
05KP-Aldh1a11R8bselection 0
10KP-Aldh1a11R10selection 0



Experiment Documentation

Experimenter Katie Pelch
Date of Experiment 10/18/13
Project name RWPE1 Endpoint Comparison
Tissue RWPE1
Gene or position Aldh1a1 #1