Running Bismark for sample EF03-EM03-Zygote with score_min L,0,-0.4
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	1127
Mapping efficiency:	11.3%

Sequence pairs with no alignments under any condition:	8315
Sequence pairs did not map uniquely:	558
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	326	((converted) top strand)
GA/CT/CT:	239	(complementary to (converted) top strand)
GA/CT/GA:	251	(complementary to (converted) bottom strand)
CT/GA/GA:	311	((converted) bottom strand)

Sample EF03-EM03-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF03-EM03-Zygote with score_min L,0,-0.6
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	1644
Mapping efficiency:	16.4%

Sequence pairs with no alignments under any condition:	7649
Sequence pairs did not map uniquely:	707
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	476	((converted) top strand)
GA/CT/CT:	351	(complementary to (converted) top strand)
GA/CT/GA:	350	(complementary to (converted) bottom strand)
CT/GA/GA:	467	((converted) bottom strand)

Sample EF03-EM03-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF03-EM03-Zygote with score_min L,0,-0.8
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	2080
Mapping efficiency:	20.8%

Sequence pairs with no alignments under any condition:	7085
Sequence pairs did not map uniquely:	835
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	588	((converted) top strand)
GA/CT/CT:	456	(complementary to (converted) top strand)
GA/CT/GA:	439	(complementary to (converted) bottom strand)
CT/GA/GA:	597	((converted) bottom strand)

Sample EF03-EM03-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF03-EM03-Zygote with score_min L,0,-1.0
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	2574
Mapping efficiency:	25.7%

Sequence pairs with no alignments under any condition:	6472
Sequence pairs did not map uniquely:	954
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	712	((converted) top strand)
GA/CT/CT:	583	(complementary to (converted) top strand)
GA/CT/GA:	565	(complementary to (converted) bottom strand)
CT/GA/GA:	714	((converted) bottom strand)

Sample EF03-EM03-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF03-EM03-Zygote with score_min L,-1,-0.6
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	1677
Mapping efficiency:	16.8%

Sequence pairs with no alignments under any condition:	7611
Sequence pairs did not map uniquely:	712
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	482	((converted) top strand)
GA/CT/CT:	359	(complementary to (converted) top strand)
GA/CT/GA:	358	(complementary to (converted) bottom strand)
CT/GA/GA:	478	((converted) bottom strand)

Sample EF03-EM03-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample EF03-EM03-Zygote completed.