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: 63030 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99921835 Sequence pairs did not map uniquely: 15135 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: 36902 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 26128 ((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: 42238065 Mapping efficiency: 42.2% Sequence pairs with no alignments under any condition: 47296525 Sequence pairs did not map uniquely: 10465410 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: 21163090 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 21074970 ((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: 834762 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 98956984 Sequence pairs did not map uniquely: 208254 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: 418178 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 416583 ((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: 750430 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 99071973 Sequence pairs did not map uniquely: 177597 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: 376879 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 373551 ((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: 60570279 Mapping efficiency: 60.6% Sequence pairs with no alignments under any condition: 24907886 Sequence pairs did not map uniquely: 14521835 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30342555 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 30227721 ((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: 131002 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99836831 Sequence pairs did not map uniquely: 32167 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: 66917 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 64084 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0