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: 61184249 Mapping efficiency: 61.2% Sequence pairs with no alignments under any condition: 23837777 Sequence pairs did not map uniquely: 14977974 Sequence pairs which were discarded because genomic sequence could not be extracted: 6 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30648458 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 30535785 ((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: 60875995 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 24043733 Sequence pairs did not map uniquely: 15080272 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: 30497743 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 30378245 ((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: 46458438 Mapping efficiency: 46.5% Sequence pairs with no alignments under any condition: 43480357 Sequence pairs did not map uniquely: 10061205 Sequence pairs which were discarded because genomic sequence could not be extracted: 11 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 46443315 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 15112 ((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: 15206047 Mapping efficiency: 15.2% Sequence pairs with no alignments under any condition: 81192518 Sequence pairs did not map uniquely: 3601435 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 7616159 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 7589886 ((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: 283383 Mapping efficiency: 0.3% Sequence pairs with no alignments under any condition: 99648473 Sequence pairs did not map uniquely: 68144 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: 142802 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 140581 ((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: 744708 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99072928 Sequence pairs did not map uniquely: 182364 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: 374615 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 370092 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0