Category	AS-0.2	AS-0.6	AS-1	AS-1I60	AS-1.2I60	AS-2
Sequence pairs analysed in total:	100000	100000	100000	100000	100000	100000
Number of paired-end alignments with a unique best hit:	33792	50404	60242	57640	64243	78584
Mapping efficiency:	33.8% 	50.4% 	60.2% 	57.6% 	64.2% 	78.6% 
Sequence pairs with no alignments under any condition:	52674	30450	19648	23377	17021	187
Sequence pairs did not map uniquely:	13534	19146	20110	18983	18736	21229
Sequence pairs which were discarded because genomic sequence could not be extracted:	2	7	8	5	13	24
C methylated in CpG context:	78.3%	77.3%	74.7%	74.6%	72.4%	70.1%
C methylated in CHG context:	0.8%	1.2%	1.5%	1.6%	1.8%	2.6%
C methylated in CHH context:	1.4%	5.1%	4.2%	4.1%	4.3%	7.1%
C methylated in unknown context (CN or CHN):	27.0%	29.0%	22.0%	22.1%	20.6%	24.2%
Sequence pairs analysed in total:	100000	100000	100000	100000	100000	100000
Number of paired-end alignments with a unique best hit:	35217	50277	60607	60990	66670	77872
Mapping efficiency:	35.2% 	50.3% 	60.6% 	61.0% 	66.7% 	77.9% 
Sequence pairs with no alignments under any condition:	48948	30229	20623	19853	13370	190
Sequence pairs did not map uniquely:	15835	19494	18770	19157	19960	21938
Sequence pairs which were discarded because genomic sequence could not be extracted:	2	7	5	8	13	12
C methylated in CpG context:	77.7%	76.8%	74.4%	73.9%	72.7%	71.1%
C methylated in CHG context:	0.8%	1.3%	1.6%	1.7%	1.9%	2.6%
C methylated in CHH context:	1.6%	2.6%	3.7%	4.6%	5.6%	8.3%
C methylated in unknown context (CN or CHN):	31.0%	28.7%	21.8%	24.0%	22.5%	25.3%
Sequence pairs analysed in total:	100000	100000	100000	100000	100000	100000
Number of paired-end alignments with a unique best hit:	33128	50742	61863	55901	64030	82135
Mapping efficiency:	33.1% 	50.7% 	61.9% 	55.9% 	64.0% 	82.1% 
Sequence pairs with no alignments under any condition:	56167	26303	15515	22894	15716	137
Sequence pairs did not map uniquely:	10705	22955	22622	21205	20254	17728
Sequence pairs which were discarded because genomic sequence could not be extracted:	0	8	14	6	11	20
C methylated in CpG context:	76.9%	76.3%	75.1%	74.4%	73.7%	70.0%
C methylated in CHG context:	0.8%	1.3%	1.7%	1.7%	2.4%	2.6%
C methylated in CHH context:	1.1%	2.9%	4.1%	5.2%	5.3%	7.1%
C methylated in unknown context (CN or CHN):	24.8%	29.2%	22.8%	24.1%	23.2%	24.5%
Sequence pairs analysed in total:	100000	100000	100000	100000	100000	100000
Number of paired-end alignments with a unique best hit:	34587	46546	60714	59451	65049	76588
Mapping efficiency:	34.6% 	46.5% 	60.7% 	59.5% 	65.0% 	76.6% 
Sequence pairs with no alignments under any condition:	49537	36717	14297	23988	16751	119
Sequence pairs did not map uniquely:	15876	16737	24989	16561	18200	23293
Sequence pairs which were discarded because genomic sequence could not be extracted:	1	1	10	14	13	11
C methylated in CpG context:	78.6%	77.4%	74.3%	72.6%	73.5%	71.8%
C methylated in CHG context:	0.8%	1.3%	1.7%	1.5%	1.6%	3.2%
C methylated in CHH context:	1.4%	2.2%	4.4%	2.8%	3.5%	7.4%
C methylated in unknown context (CN or CHN):	26.3%	28.1%	23.4%	21.2%	19.3%	25.4%
Sequence pairs analysed in total:	100000	100000	100000	100000	100000	100000
Number of paired-end alignments with a unique best hit:	28259	47808	60230	56796	61488	72378
Mapping efficiency:	28.3% 	47.8% 	60.2% 	56.8% 	61.5% 	72.4% 
Sequence pairs with no alignments under any condition:	59082	33583	18606	25589	15340	158
Sequence pairs did not map uniquely:	12659	18609	21164	17615	23172	27464
Sequence pairs which were discarded because genomic sequence could not be extracted:	4	3	7	6	8	15
C methylated in CpG context:	78.9%	77.5%	75.1%	75.0%	74.5%	73.0%
C methylated in CHG context:	1.0%	1.7%	2.1%	1.7%	2.0%	2.7%
C methylated in CHH context:	1.5%	2.9%	3.9%	3.4%	7.7%	9.7%
C methylated in unknown context (CN or CHN):	33.3%	31.3%	24.2%	21.8%	24.2%	27.5%