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: 54662 Mapping efficiency: 0.1% Sequence pairs with no alignments under any condition: 99931941 Sequence pairs did not map uniquely: 13397 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: 28534 ((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: 42149770 Mapping efficiency: 42.1% Sequence pairs with no alignments under any condition: 47406533 Sequence pairs did not map uniquely: 10443697 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: 21119868 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 21029897 ((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: 845723 Mapping efficiency: 0.8% Sequence pairs with no alignments under any condition: 98943295 Sequence pairs did not map uniquely: 210982 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: 423625 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 422097 ((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: 728768 Mapping efficiency: 0.7% Sequence pairs with no alignments under any condition: 99098875 Sequence pairs did not map uniquely: 172357 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: 366031 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 362737 ((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: 60713378 Mapping efficiency: 60.7% Sequence pairs with no alignments under any condition: 24444087 Sequence pairs did not map uniquely: 14842535 Sequence pairs which were discarded because genomic sequence could not be extracted: 8 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30425359 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 30288011 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0