Processing LCo_BSr1 chr Chromosome_1 (173399226 bp) chr Chromosome_2 (140585540 bp) chr Chromosome_3 (154669058 bp) chr Chromosome_4 (155271769 bp) chr Chromosome_5 (143711894 bp) chr Chromosome_6 (146112803 bp) chr Chromosome_7 (140080477 bp) chr Chromosome_8 (134086722 bp) chr Chromosome_9 (133209816 bp) chr Chromosome_10 (132883123 bp) chr Chromosome_11 (131458407 bp) chr Chromosome_12 (123051472 bp) chr Chromosome_13 (113386651 bp) chr Chromosome_14 (117416392 bp) Number of paired-end alignments with a unique best hit: 158868 Mapping efficiency: 0.2% Sequence pairs with no alignments under any condition: 99802735 Sequence pairs did not map uniquely: 38397 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: 72202 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 86666 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Processing LCo_BSr2 chr Chromosome_1 (173399226 bp) chr Chromosome_2 (140585540 bp) chr Chromosome_3 (154669058 bp) chr Chromosome_4 (155271769 bp) chr Chromosome_5 (143711894 bp) chr Chromosome_6 (146112803 bp) chr Chromosome_7 (140080477 bp) chr Chromosome_8 (134086722 bp) chr Chromosome_9 (133209816 bp) chr Chromosome_10 (132883123 bp) chr Chromosome_11 (131458407 bp) chr Chromosome_12 (123051472 bp) chr Chromosome_13 (113386651 bp) chr Chromosome_14 (117416392 bp) Number of paired-end alignments with a unique best hit: 42105979 Mapping efficiency: 42.1% Sequence pairs with no alignments under any condition: 47461111 Sequence pairs did not map uniquely: 10432910 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 21097963 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 21008011 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Processing LCo_BSr3 chr Chromosome_1 (173399226 bp) chr Chromosome_2 (140585540 bp) chr Chromosome_3 (154669058 bp) chr Chromosome_4 (155271769 bp) chr Chromosome_5 (143711894 bp) chr Chromosome_6 (146112803 bp) chr Chromosome_7 (140080477 bp) chr Chromosome_8 (134086722 bp) chr Chromosome_9 (133209816 bp) chr Chromosome_10 (132883123 bp) chr Chromosome_11 (131458407 bp) chr Chromosome_12 (123051472 bp) chr Chromosome_13 (113386651 bp) chr Chromosome_14 (117416392 bp) Number of paired-end alignments with a unique best hit: 878051 Mapping efficiency: 0.9% Sequence pairs with no alignments under any condition: 98903054 Sequence pairs did not map uniquely: 218895 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 440844 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 437206 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Processing LYa_BSr1 chr Chromosome_1 (173399226 bp) chr Chromosome_2 (140585540 bp) chr Chromosome_3 (154669058 bp) chr Chromosome_4 (155271769 bp) chr Chromosome_5 (143711894 bp) chr Chromosome_6 (146112803 bp) chr Chromosome_7 (140080477 bp) chr Chromosome_8 (134086722 bp) chr Chromosome_9 (133209816 bp) chr Chromosome_10 (132883123 bp) chr Chromosome_11 (131458407 bp) chr Chromosome_12 (123051472 bp) chr Chromosome_13 (113386651 bp) chr Chromosome_14 (117416392 bp) Number of paired-end alignments with a unique best hit: 75823 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99906530 Sequence pairs did not map uniquely: 17647 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: 38936 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 36887 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Processing LYa_BSr2 chr Chromosome_1 (173399226 bp) chr Chromosome_2 (140585540 bp) chr Chromosome_3 (154669058 bp) chr Chromosome_4 (155271769 bp) chr Chromosome_5 (143711894 bp) chr Chromosome_6 (146112803 bp) chr Chromosome_7 (140080477 bp) chr Chromosome_8 (134086722 bp) chr Chromosome_9 (133209816 bp) chr Chromosome_10 (132883123 bp) chr Chromosome_11 (131458407 bp) chr Chromosome_12 (123051472 bp) chr Chromosome_13 (113386651 bp) chr Chromosome_14 (117416392 bp) Number of paired-end alignments with a unique best hit: 21127 Mapping efficiency: 0.0% Sequence pairs with no alignments under any condition: 99973717 Sequence pairs did not map uniquely: 5156 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: 11594 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 9533 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Processing LYa_BSr3 chr Chromosome_1 (173399226 bp) chr Chromosome_2 (140585540 bp) chr Chromosome_3 (154669058 bp) chr Chromosome_4 (155271769 bp) chr Chromosome_5 (143711894 bp) chr Chromosome_6 (146112803 bp) chr Chromosome_7 (140080477 bp) chr Chromosome_8 (134086722 bp) chr Chromosome_9 (133209816 bp) chr Chromosome_10 (132883123 bp) chr Chromosome_11 (131458407 bp) chr Chromosome_12 (123051472 bp) chr Chromosome_13 (113386651 bp) chr Chromosome_14 (117416392 bp) Number of paired-end alignments with a unique best hit: 58214606 Mapping efficiency: 58.2% Sequence pairs with no alignments under any condition: 27556078 Sequence pairs did not map uniquely: 14229316 Sequence pairs which were discarded because genomic sequence could not be extracted: 7 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 29169770 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 29044829 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0