Running Bismark for sample EF04-EM04-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: 510 Mapping efficiency: 5.1% Sequence pairs with no alignments under any condition: 9241 Sequence pairs did not map uniquely: 249 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: 125 ((converted) top strand) GA/CT/CT: 123 (complementary to (converted) top strand) GA/CT/GA: 129 (complementary to (converted) bottom strand) CT/GA/GA: 133 ((converted) bottom strand) Sample EF04-EM04-Zygote with score_min L,0,-0.4 processed successfully. Running Bismark for sample EF04-EM04-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: 863 Mapping efficiency: 8.6% Sequence pairs with no alignments under any condition: 8761 Sequence pairs did not map uniquely: 376 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: 201 ((converted) top strand) GA/CT/CT: 212 (complementary to (converted) top strand) GA/CT/GA: 224 (complementary to (converted) bottom strand) CT/GA/GA: 226 ((converted) bottom strand) Sample EF04-EM04-Zygote with score_min L,0,-0.6 processed successfully. Running Bismark for sample EF04-EM04-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: 1384 Mapping efficiency: 13.8% Sequence pairs with no alignments under any condition: 8071 Sequence pairs did not map uniquely: 545 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: 343 ((converted) top strand) GA/CT/CT: 352 (complementary to (converted) top strand) GA/CT/GA: 347 (complementary to (converted) bottom strand) CT/GA/GA: 342 ((converted) bottom strand) Sample EF04-EM04-Zygote with score_min L,0,-0.8 processed successfully. Running Bismark for sample EF04-EM04-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: 2180 Mapping efficiency: 21.8% Sequence pairs with no alignments under any condition: 7056 Sequence pairs did not map uniquely: 764 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: 539 ((converted) top strand) GA/CT/CT: 545 (complementary to (converted) top strand) GA/CT/GA: 555 (complementary to (converted) bottom strand) CT/GA/GA: 541 ((converted) bottom strand) Sample EF04-EM04-Zygote with score_min L,0,-1.0 processed successfully. Running Bismark for sample EF04-EM04-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: 882 Mapping efficiency: 8.8% Sequence pairs with no alignments under any condition: 8721 Sequence pairs did not map uniquely: 397 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: 209 ((converted) top strand) GA/CT/CT: 219 (complementary to (converted) top strand) GA/CT/GA: 227 (complementary to (converted) bottom strand) CT/GA/GA: 227 ((converted) bottom strand) Sample EF04-EM04-Zygote with score_min L,-1,-0.6 processed successfully. All tests for sample EF04-EM04-Zygote completed.