Mercurial > repos > iuc > breseq
diff test-data/gdout.txt @ 3:0d18a3ba2d1c draft default tip
"planemo upload commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2022 08:30:52 +0000 |
| parents | 82fb5e3bb93e |
| children |
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--- a/test-data/gdout.txt Wed Apr 07 12:17:45 2021 +0000 +++ b/test-data/gdout.txt Mon Apr 04 08:30:52 2022 +0000 @@ -1,31 +1,489 @@ #=GENOME_DIFF 1.0 #=TITLE smallest -#=CREATED 12:47:14 07 Apr 2021 +#=CREATED 09:02:10 11 Oct 2021 #=PROGRAM breseq 0.35.5 -#=COMMAND breseq --num-processors 1 -o results --reference /home/berntm/.planemo/planemo_tmp_c9ga3mbq/test-data/lambda.gbk /tmp/tmpld3eebea/files/8/e/1/dataset_8e1ab48f-6786-4ed7-bf44-beec17749bb3.dat --name smallest -#=REFSEQ /home/berntm/.planemo/planemo_tmp_c9ga3mbq/test-data/lambda.gbk -#=READSEQ /tmp/tmpld3eebea/files/8/e/1/dataset_8e1ab48f-6786-4ed7-bf44-beec17749bb3.dat -#=CONVERTED-BASES 250000 -#=CONVERTED-READS 5000 -#=INPUT-BASES 250000 -#=INPUT-READS 5000 -#=MAPPED-BASES 242755 -#=MAPPED-READS 4870 -INS 1 11 NC_001416 41405 GCGGCGGCG repeat_length=3 repeat_new_copies=5 repeat_ref_copies=2 repeat_seq=GCG -DEL 2 8,12 NC_001416 41601 3 repeat_length=3 repeat_new_copies=1 repeat_ref_copies=2 repeat_seq=AAC -INS 3 13 NC_001416 41716 TTTT repeat_length=1 repeat_new_copies=9 repeat_ref_copies=5 repeat_seq=T -DEL 4 9,14 NC_001416 44075 4 repeat_length=4 repeat_new_copies=1 repeat_ref_copies=2 repeat_seq=CAAA -SNP 5 6 NC_001416 47317 T -RA 6 . NC_001416 47317 0 N T consensus_score=105.6 frequency=1 major_base=T major_cov=17/17 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=17/17 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=17/17 -MC 7 . NC_001416 1 38810 0 0 left_inside_cov=0 left_outside_cov=NA right_inside_cov=10 right_outside_cov=13 -MC 8 . NC_001416 41601 41603 0 0 left_inside_cov=0 left_outside_cov=29 right_inside_cov=0 right_outside_cov=28 -MC 9 . NC_001416 44075 44078 0 0 left_inside_cov=0 left_outside_cov=28 right_inside_cov=0 right_outside_cov=27 -MC 10 . NC_001416 48475 48502 0 0 left_inside_cov=10 left_outside_cov=12 right_inside_cov=0 right_outside_cov=NA -JC 11 . NC_001416 41398 1 NC_001416 41405 -1 -1 alignment_overlap=-1 coverage_minus=5 coverage_plus=18 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=48 key=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0 max_left=44 max_left_minus=38 max_left_plus=44 max_min_left=24 max_min_left_minus=23 max_min_left_plus=24 max_min_right=23 max_min_right_minus=11 max_min_right_plus=23 max_pos_hash_score=96 max_right=47 max_right_minus=34 max_right_plus=47 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.10 new_junction_read_count=27 polymorphism_frequency=9.168e-01 pos_hash_score=21 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.04 side_1_overlap=0 side_1_possible_overlap_registers=49 side_1_read_count=1 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.16 side_2_overlap=0 side_2_possible_overlap_registers=49 side_2_read_count=4 side_2_redundant=0 total_non_overlap_reads=23 unique_read_sequence=C -JC 12 . NC_001416 41600 -1 NC_001416 41604 1 0 alignment_overlap=4 coverage_minus=14 coverage_plus=8 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=45 key=NC_001416__41600__-1__NC_001416__41600__1__4____50__50__0__0 max_left=42 max_left_minus=42 max_left_plus=38 max_min_left=22 max_min_left_minus=20 max_min_left_plus=22 max_min_right=20 max_min_right_minus=12 max_min_right_plus=20 max_pos_hash_score=90 max_right=44 max_right_minus=44 max_right_plus=37 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.00 new_junction_read_count=23 polymorphism_frequency=1.000e+00 pos_hash_score=19 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=4 side_1_possible_overlap_registers=49 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=45 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=22 -JC 13 . NC_001416 41712 1 NC_001416 41715 -1 0 alignment_overlap=1 coverage_minus=11 coverage_plus=11 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=48 key=NC_001416__41712__1__NC_001416__41716__-1__1____50__50__0__0 max_left=48 max_left_minus=39 max_left_plus=48 max_min_left=21 max_min_left_minus=21 max_min_left_plus=18 max_min_right=23 max_min_right_minus=23 max_min_right_plus=23 max_pos_hash_score=96 max_right=46 max_right_minus=34 max_right_plus=46 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.06 new_junction_read_count=26 polymorphism_frequency=8.826e-01 pos_hash_score=21 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.16 side_1_overlap=1 side_1_possible_overlap_registers=49 side_1_read_count=4 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.12 side_2_overlap=0 side_2_possible_overlap_registers=48 side_2_read_count=3 side_2_redundant=0 total_non_overlap_reads=22 -JC 14 . NC_001416 44074 -1 NC_001416 44079 1 0 alignment_overlap=5 coverage_minus=19 coverage_plus=5 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=44 key=NC_001416__44074__-1__NC_001416__44074__1__5____50__50__0__0 max_left=44 max_left_minus=43 max_left_plus=44 max_min_left=21 max_min_left_minus=21 max_min_left_plus=18 max_min_right=22 max_min_right_minus=22 max_min_right_plus=12 max_pos_hash_score=88 max_right=43 max_right_minus=43 max_right_plus=27 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.11 new_junction_read_count=25 polymorphism_frequency=1.000e+00 pos_hash_score=20 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=5 side_1_possible_overlap_registers=49 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=44 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=24 -UN 15 . NC_001416 1 38807 -UN 16 . NC_001416 41601 41603 -UN 17 . NC_001416 44075 44078 -UN 18 . NC_001416 48488 48502 +#=COMMAND breseq --num-processors 1 -o results --reference /home/berntm/.planemo/planemo_tmp_761ytc5o/test-data/lambda.gbk /tmp/tmpxwfwo8j7/files/c/c/a/dataset_cca0e808-86ed-4449-ad0e-b35d828c94e7.dat --name smallest +#=REFSEQ /home/berntm/.planemo/planemo_tmp_761ytc5o/test-data/lambda.gbk +#=READSEQ /tmp/tmpxwfwo8j7/files/c/c/a/dataset_cca0e808-86ed-4449-ad0e-b35d828c94e7.dat +#=CONVERTED-BASES 62500 +#=CONVERTED-READS 1250 +#=INPUT-BASES 62500 +#=INPUT-READS 1250 +#=MAPPED-BASES 61052 +#=MAPPED-READS 1225 +INS 1 9 NC_001416 41405 GCGGCGGCG repeat_length=3 repeat_new_copies=5 repeat_ref_copies=2 repeat_seq=GCG +DEL 2 6,10 NC_001416 41601 3 repeat_length=3 repeat_new_copies=1 repeat_ref_copies=2 repeat_seq=AAC +SNP 3 4 NC_001416 47317 T +RA 4 . NC_001416 47317 0 N T consensus_score=31.3 frequency=1 major_base=T major_cov=7/5 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=7/5 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=7/5 +MC 5 . NC_001416 1 38811 0 0 left_inside_cov=0 left_outside_cov=NA right_inside_cov=1 right_outside_cov=2 +MC 6 . NC_001416 41601 41603 0 0 left_inside_cov=0 left_outside_cov=8 right_inside_cov=0 right_outside_cov=7 +MC 7 . NC_001416 48305 48312 0 0 left_inside_cov=1 left_outside_cov=2 right_inside_cov=1 right_outside_cov=2 +MC 8 . NC_001416 48485 48502 0 0 left_inside_cov=1 left_outside_cov=2 right_inside_cov=0 right_outside_cov=NA +JC 9 . NC_001416 41398 1 NC_001416 41405 -1 -1 alignment_overlap=-1 coverage_minus=2 coverage_plus=4 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=48 key=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0 max_left=38 max_left_minus=38 max_left_plus=38 max_min_left=23 max_min_left_minus=23 max_min_left_plus=17 max_min_right=11 max_min_right_minus=11 max_min_right_plus=11 max_pos_hash_score=96 max_right=47 max_right_minus=26 max_right_plus=47 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.14 new_junction_read_count=7 polymorphism_frequency=9.346e-01 pos_hash_score=6 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=49 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.16 side_2_overlap=0 side_2_possible_overlap_registers=49 side_2_read_count=1 side_2_redundant=0 total_non_overlap_reads=6 unique_read_sequence=C +JC 10 . NC_001416 41600 -1 NC_001416 41604 1 0 alignment_overlap=4 coverage_minus=5 coverage_plus=1 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=45 key=NC_001416__41600__-1__NC_001416__41600__1__4____50__50__0__0 max_left=20 max_left_minus=20 max_left_plus=10 max_min_left=20 max_min_left_minus=20 max_min_left_plus=10 max_min_right=0 max_min_right_minus=0 max_min_right_plus=0 max_pos_hash_score=90 max_right=44 max_right_minus=44 max_right_plus=36 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.05 new_junction_read_count=6 polymorphism_frequency=1.000e+00 pos_hash_score=5 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=4 side_1_possible_overlap_registers=49 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=45 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=6 +UN 11 . 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