#=GENOME_DIFF 1.0 #=CREATED 01:11:51 08 Apr 2020 #=PROGRAM breseq 0.33.1 revision 8505477f25b3 #=COMMAND /usr/bin/breseq-0.33.1-Linux-x86_64/bin/breseq -p -j 1 --consensus-frequency-cutoff=0.75 --require-match-fraction=0.95 -o breseq_processes/10 -r /var/data/GCA_000011525.1_ASM1152v1_genomic.gb /var/alemutpipe-outputs/good/ERR1440903_R1.good.fq /var/alemutpipe-outputs/good/ERR1440903_R2.good.fq #=REFSEQ /var/data/GCA_000011525.1_ASM1152v1_genomic.gb #=READSEQ /var/alemutpipe-outputs/good/ERR1440903_R1.good.fq #=READSEQ /var/alemutpipe-outputs/good/ERR1440903_R2.good.fq #=CONVERTED-BASES 74631670 #=CONVERTED-READS 769492 #=INPUT-BASES 74631670 #=INPUT-READS 769492 #=MAPPED-BASES 73583007 #=MAPPED-READS 759064 SNP 1 9 BX571857 10884 A frequency=3.33249092e-01 SNP 2 10 BX571857 292191 A frequency=2.87289619e-01 SNP 3 11 BX571857 692784 A frequency=2.48363495e-01 SNP 4 12 BX571857 797809 T frequency=3.18176270e-01 SNP 5 13 BX571857 848832 G frequency=2.33383656e-01 SNP 6 14 BX571857 1252438 C frequency=1 SNP 7 15 BX571857 1868342 A frequency=1 INS 8 16 BX571858 20628 G frequency=1 insert_position=1 RA 9 . BX571857 10884 0 G A bias_e_value=2820450 bias_p_value=1 consensus_score=46.9 fisher_strand_p_value=1 frequency=3.33249092e-01 ks_quality_p_value=1 major_base=G major_cov=11/11 major_frequency=6.66750908e-01 minor_base=A minor_cov=6/5 new_cov=6/5 polymorphism_frequency=3.33249092e-01 polymorphism_score=35.0 prediction=polymorphism ref_cov=11/11 total_cov=17/16 RA 10 . BX571857 292191 0 G A bias_e_value=2107150 bias_p_value=0.747096 consensus_score=32.3 fisher_strand_p_value=0.392639 frequency=2.87289619e-01 ks_quality_p_value=0.966268 major_base=G major_cov=6/11 major_frequency=7.12710381e-01 minor_base=A minor_cov=4/3 new_cov=4/3 polymorphism_frequency=2.87289619e-01 polymorphism_score=18.2 prediction=polymorphism ref_cov=6/11 total_cov=10/15 RA 11 . BX571857 692784 0 G A bias_e_value=849117 bias_p_value=0.301057 consensus_score=66.4 fisher_strand_p_value=0.0876629 frequency=2.48363495e-01 ks_quality_p_value=1 major_base=G major_cov=6/18 major_frequency=7.51636505e-01 minor_base=A minor_cov=5/3 new_cov=5/3 polymorphism_frequency=2.48363495e-01 polymorphism_score=22.6 prediction=polymorphism ref_cov=6/18 total_cov=11/21 RA 12 . BX571857 797809 0 C T bias_e_value=2817990 bias_p_value=0.999125 consensus_score=28.3 fisher_strand_p_value=1 frequency=3.18176270e-01 ks_quality_p_value=0.958463 major_base=C major_cov=10/5 major_frequency=6.81823730e-01 minor_base=T minor_cov=5/2 new_cov=5/2 polymorphism_frequency=3.18176270e-01 polymorphism_score=22.1 prediction=polymorphism ref_cov=10/5 total_cov=15/7 RA 13 . BX571857 848832 0 T G bias_e_value=2778780 bias_p_value=0.985224 consensus_score=62.5 fisher_strand_p_value=1 frequency=2.33383656e-01 ks_quality_p_value=0.833094 major_base=T major_cov=7/16 major_frequency=7.66616344e-01 minor_base=G minor_cov=2/5 new_cov=2/5 polymorphism_frequency=2.33383656e-01 polymorphism_score=24.4 prediction=polymorphism ref_cov=7/16 total_cov=9/21 RA 14 . BX571857 1252438 0 T C consensus_score=56.2 frequency=1 major_base=C major_cov=6/8 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=6/8 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=6/8 RA 15 . BX571857 1868342 0 G A consensus_score=115.6 frequency=1 major_base=A major_cov=9/19 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=9/19 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=9/19 RA 16 . BX571858 20628 1 . G consensus_score=51.9 frequency=1 major_base=G major_cov=5/8 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=5/8 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=5/8 MC 17 . BX571857 936992 937082 0 0 left_inside_cov=5 left_outside_cov=6 right_inside_cov=5 right_outside_cov=7 MC 18 . BX571857 1502596 1502688 0 0 left_inside_cov=4 left_outside_cov=6 right_inside_cov=5 right_outside_cov=6 MC 19 . BX571857 1995792 1995888 0 0 left_inside_cov=5 left_outside_cov=6 right_inside_cov=5 right_outside_cov=6 MC 20 . BX571858 20652 20652 0 0 left_inside_cov=0 left_outside_cov=16 right_inside_cov=0 right_outside_cov=NA JC 21 . BX571857 1 1 BX571857 2799802 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=17 coverage_plus=15 flanking_left=97 flanking_right=97 frequency=1 junction_possible_overlap_registers=85 key=BX571857__1__1__BX571857__2799802__-1__0____97__97__0__0 max_left=90 max_left_minus=90 max_left_plus=88 max_min_left=43 max_min_left_minus=43 max_min_left_plus=41 max_min_right=46 max_min_right_minus=46 max_min_right_plus=44 max_pos_hash_score=172 max_right=89 max_right_minus=89 max_right_plus=87 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.38 new_junction_read_count=32 polymorphism_frequency=1.00000000e+00 pos_hash_score=25 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=85 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=85 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=32 JC 22 . BX571857 980997 1 BX571857 1025750 -1 0 alignment_overlap=27 coverage_minus=3 coverage_plus=2 flanking_left=97 flanking_right=97 frequency=NA junction_possible_overlap_registers=58 key=BX571857__980997__1__BX571857__1025777__-1__27____97__97__0__0 max_left=55 max_left_minus=55 max_left_plus=42 max_min_left=34 max_min_left_minus=34 max_min_left_plus=33 max_min_right=28 max_min_right_minus=15 max_min_right_plus=28 max_pos_hash_score=118 max_right=38 max_right_minus=38 max_right_plus=37 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.32 new_junction_read_count=5 polymorphism_frequency=NA pos_hash_score=5 prediction=unknown side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=27 side_1_read_count=NA side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=0 total_non_overlap_reads=5 JC 23 . BX571858 1 1 BX571858 20651 -1 0 alignment_overlap=1 coverage_minus=4 coverage_plus=9 flanking_left=97 flanking_right=97 frequency=1 junction_possible_overlap_registers=84 key=BX571858__1__1__BX571858__20652__-1__1____97__97__0__0 max_left=89 max_left_minus=62 max_left_plus=89 max_min_left=43 max_min_left_minus=26 max_min_left_plus=43 max_min_right=39 max_min_right_minus=33 max_min_right_plus=39 max_pos_hash_score=170 max_right=83 max_right_minus=83 max_right_plus=66 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.99 new_junction_read_count=13 polymorphism_frequency=1.00000000e+00 pos_hash_score=12 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=1 side_1_possible_overlap_registers=85 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=84 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=13 UN 24 . BX571857 53939 53940 UN 25 . BX571857 53945 53945 UN 26 . BX571857 53947 53947 UN 27 . BX571857 129722 129776 UN 28 . BX571857 203082 203095 UN 29 . BX571857 203107 203124 UN 30 . BX571857 207951 207951 UN 31 . BX571857 207966 207966 UN 32 . BX571857 207996 207996 UN 33 . BX571857 304208 304208 UN 34 . BX571857 304211 304211 UN 35 . BX571857 304214 304234 UN 36 . BX571857 304236 304236 UN 37 . BX571857 322290 322290 UN 38 . BX571857 322293 322293 UN 39 . BX571857 322301 322301 UN 40 . BX571857 322802 322810 UN 41 . BX571857 323003 323003 UN 42 . BX571857 323994 323995 UN 43 . BX571857 323998 324008 UN 44 . BX571857 324562 324571 UN 45 . BX571857 324574 324574 UN 46 . BX571857 324577 324579 UN 47 . BX571857 324584 324584 UN 48 . BX571857 324599 324599 UN 49 . BX571857 324601 324601 UN 50 . BX571857 324603 324604 UN 51 . BX571857 324610 324610 UN 52 . BX571857 324612 324612 UN 53 . BX571857 324615 324618 UN 54 . BX571857 440689 440771 UN 55 . BX571857 490125 491797 UN 56 . 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