#=GENOME_DIFF 1.0 #=CREATED 21:07:28 07 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/4 -r /var/data/GCA_000011525.1_ASM1152v1_genomic.gb /var/alemutpipe-outputs/good/ERR1579171_R1.good.fq /var/alemutpipe-outputs/good/ERR1579171_R2.good.fq #=REFSEQ /var/data/GCA_000011525.1_ASM1152v1_genomic.gb #=READSEQ /var/alemutpipe-outputs/good/ERR1579171_R1.good.fq #=READSEQ /var/alemutpipe-outputs/good/ERR1579171_R2.good.fq #=CONVERTED-BASES 472939986 #=CONVERTED-READS 4876272 #=INPUT-BASES 472939986 #=INPUT-READS 4876272 #=MAPPED-BASES 467161797 #=MAPPED-READS 4818479 SNP 1 12 BX571857 4422 A frequency=5.13534546e-02 SNP 2 13 BX571857 423924 A frequency=4.42271709e-01 SNP 3 14 BX571857 431505 C frequency=7.36513138e-02 SNP 4 15 BX571857 596994 C frequency=8.69083405e-02 SNP 5 16 BX571857 605157 C frequency=5.19680977e-02 SNP 6 17 BX571857 1252438 C frequency=1 SNP 7 18 BX571857 1472161 G frequency=5.06472588e-02 SNP 8 19 BX571857 1472392 T frequency=5.79819679e-02 SNP 9 20 BX571857 1868342 A frequency=1 SNP 10 21 BX571857 2700227 G frequency=5.72881699e-02 INS 11 22 BX571858 20628 G frequency=1 insert_position=1 RA 12 . BX571857 4422 0 C A bias_e_value=2489.76 bias_p_value=0.00088275 consensus_score=1001.7 fisher_strand_p_value=8.51128e-05 frequency=5.13534546e-02 ks_quality_p_value=1 major_base=C major_cov=137/95 major_frequency=9.48646545e-01 minor_base=A minor_cov=2/16 new_cov=2/16 polymorphism_frequency=5.13534546e-02 polymorphism_score=3.3 prediction=polymorphism ref_cov=137/95 total_cov=139/111 RA 13 . BX571857 423924 0 G A bias_e_value=2820450 bias_p_value=1 consensus_score=51.9 fisher_strand_p_value=1 frequency=4.42271709e-01 ks_quality_p_value=1 major_base=G major_cov=46/27 major_frequency=5.57728291e-01 minor_base=A minor_cov=37/21 new_cov=37/21 polymorphism_frequency=4.42271709e-01 polymorphism_score=225.3 prediction=polymorphism ref_cov=46/27 total_cov=83/48 RA 14 . BX571857 431505 0 T C bias_e_value=1841280 bias_p_value=0.65283 consensus_score=600.4 fisher_strand_p_value=0.293121 frequency=7.36513138e-02 ks_quality_p_value=1 major_base=T major_cov=71/84 major_frequency=9.26348686e-01 minor_base=C minor_cov=10/6 new_cov=10/6 polymorphism_frequency=7.36513138e-02 polymorphism_score=4.7 prediction=polymorphism ref_cov=71/84 total_cov=82/92 RA 15 . BX571857 596994 0 T C bias_e_value=72300.2 bias_p_value=0.0256342 consensus_score=534.8 fisher_strand_p_value=0.00391836 frequency=8.69083405e-02 ks_quality_p_value=1 major_base=T major_cov=73/58 major_frequency=9.13091660e-01 minor_base=C minor_cov=2/12 new_cov=2/12 polymorphism_frequency=8.69083405e-02 polymorphism_score=10.2 prediction=polymorphism ref_cov=73/58 total_cov=77/71 RA 16 . BX571857 605157 0 T C bias_e_value=719047 bias_p_value=0.25494 consensus_score=679.6 fisher_strand_p_value=0.0695463 frequency=5.19680977e-02 ks_quality_p_value=1 major_base=T major_cov=76/93 major_frequency=9.48031902e-01 minor_base=C minor_cov=9/3 new_cov=9/3 polymorphism_frequency=5.19680977e-02 polymorphism_score=3.4 prediction=polymorphism ref_cov=76/93 total_cov=86/96 RA 17 . BX571857 1252438 0 T C consensus_score=573.5 frequency=1 major_base=C major_cov=79/51 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=79/51 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=79/51 RA 18 . BX571857 1472161 0 T G bias_e_value=2368900 bias_p_value=0.839902 consensus_score=705.0 fisher_strand_p_value=0.515155 frequency=5.06472588e-02 ks_quality_p_value=0.952151 major_base=T major_cov=74/94 major_frequency=9.49352741e-01 minor_base=G minor_cov=5/4 new_cov=5/4 polymorphism_frequency=5.06472588e-02 polymorphism_score=21.8 prediction=polymorphism ref_cov=74/94 total_cov=80/98 RA 19 . BX571857 1472392 0 G T bias_e_value=661249 bias_p_value=0.234448 consensus_score=672.9 fisher_strand_p_value=0.0626896 frequency=5.79819679e-02 ks_quality_p_value=0.989282 major_base=G major_cov=94/69 major_frequency=9.42018032e-01 minor_base=T minor_cov=3/8 new_cov=3/8 polymorphism_frequency=5.79819679e-02 polymorphism_score=21.3 prediction=polymorphism ref_cov=94/69 total_cov=97/77 RA 20 . BX571857 1868342 0 G A consensus_score=648.5 frequency=1 major_base=A major_cov=67/75 major_frequency=1.00000000e+00 minor_base=G minor_cov=1/0 new_cov=67/75 polymorphism_frequency=1.00000000e+00 polymorphism_reject=SCORE_CUTOFF,FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=-6.5 prediction=consensus ref_cov=1/0 total_cov=68/75 RA 21 . BX571857 2700227 0 A G bias_e_value=93113.9 bias_p_value=0.0330138 consensus_score=614.8 fisher_strand_p_value=0.00528885 frequency=5.72881699e-02 ks_quality_p_value=1 major_base=A major_cov=64/94 major_frequency=9.42711830e-01 minor_base=G minor_cov=10/2 new_cov=10/2 polymorphism_frequency=5.72881699e-02 polymorphism_score=2.3 prediction=polymorphism ref_cov=64/94 total_cov=74/97 RA 22 . BX571858 20628 1 . G consensus_score=965.5 frequency=1 major_base=G major_cov=107/110 major_frequency=1.00000000e+00 minor_base=N minor_cov=0/0 new_cov=107/110 polymorphism_frequency=1.00000000e+00 polymorphism_reject=FREQUENCY_CUTOFF,VARIANT_STRAND_COVERAGE polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=107/110 MC 23 . BX571858 20652 20652 0 0 left_inside_cov=0 left_outside_cov=249 right_inside_cov=0 right_outside_cov=NA JC 24 . BX571857 1 1 BX571857 2799802 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=58 coverage_plus=61 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=91 max_left_minus=90 max_left_plus=91 max_min_left=48 max_min_left_minus=48 max_min_left_plus=47 max_min_right=48 max_min_right_minus=48 max_min_right_plus=46 max_pos_hash_score=172 max_right=91 max_right_minus=90 max_right_plus=91 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.81 new_junction_read_count=119 polymorphism_frequency=1.00000000e+00 pos_hash_score=79 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=119 JC 25 . BX571857 980997 1 BX571857 1025750 -1 0 alignment_overlap=27 coverage_minus=7 coverage_plus=7 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=64 max_left_minus=62 max_left_plus=64 max_min_left=34 max_min_left_minus=34 max_min_left_plus=27 max_min_right=29 max_min_right_minus=21 max_min_right_plus=29 max_pos_hash_score=118 max_right=62 max_right_minus=62 max_right_plus=61 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.14 new_junction_read_count=14 polymorphism_frequency=NA pos_hash_score=13 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=14 JC 26 . BX571858 1 1 BX571858 20651 -1 0 alignment_overlap=1 coverage_minus=100 coverage_plus=114 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=89 max_left_plus=89 max_min_left=47 max_min_left_minus=47 max_min_left_plus=46 max_min_right=47 max_min_right_minus=47 max_min_right_plus=43 max_pos_hash_score=170 max_right=89 max_right_minus=89 max_right_plus=89 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.13 new_junction_read_count=220 polymorphism_frequency=1.00000000e+00 pos_hash_score=111 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=214 UN 27 . BX571857 129741 129772 UN 28 . BX571857 440699 440760 UN 29 . BX571857 490131 491787 UN 30 . BX571857 491955 493541 UN 31 . BX571857 493727 495119 UN 32 . BX571857 534388 535777 UN 33 . BX571857 536215 539316 UN 34 . BX571857 539552 541195 UN 35 . BX571857 541374 544564 UN 36 . BX571857 1204138 1204155 UN 37 . BX571857 1442238 1442266 UN 38 . BX571857 1509346 1509351 UN 39 . BX571857 1880841 1880902 UN 40 . BX571857 1938579 1940043 UN 41 . BX571857 1940225 1941805 UN 42 . BX571857 1942172 1942339 UN 43 . BX571857 1942607 1943538 UN 44 . BX571857 2116340 2117798 UN 45 . BX571857 2117981 2118130 UN 46 . BX571857 2118316 2119824 UN 47 . BX571857 2119921 2121220 UN 48 . BX571857 2121406 2121482 UN 49 . BX571857 2194810 2194838 UN 50 . BX571857 2229941 2229941 UN 51 . BX571857 2229943 2229943 UN 52 . BX571857 2229945 2232499 UN 53 . BX571857 2232681 2233248 UN 54 . BX571857 2233439 2234629 UN 55 . BX571857 2234813 2234953 UN 56 . BX571857 2351159 2351161 UN 57 . BX571857 2549805 2549878 UN 58 . BX571857 2550273 2551894 UN 59 . BX571857 2778148 2778149 UN 60 . BX571857 2778331 2778338 UN 61 . BX571857 2778897 2778900 UN 62 . BX571857 2779268 2779271 UN 63 . BX571858 20652 20652