#=GENOME_DIFF 1.0 #=CREATED 16:38:53 16 Jan 2023 #=PROGRAM breseq 0.35.4 revision f352f80f4bc9 #=COMMAND /usr/bin/breseq-0.35.4-Linux-x86_64/bin/breseq -j 2 --consensus-frequency-cutoff=0.75 --require-match-fraction=0.95 -o breseq_processes/0 -r /var/data/Ecoli_B_REL606.gb /var/alemutpipe-outputs/good/SRR333728_R1.good.fq /var/alemutpipe-outputs/good/SRR333728_R2.good.fq #=REFSEQ /var/data/Ecoli_B_REL606.gb #=READSEQ /var/alemutpipe-outputs/good/SRR333728_R1.good.fq #=READSEQ /var/alemutpipe-outputs/good/SRR333728_R2.good.fq #=CONVERTED-BASES 1263111136 #=CONVERTED-READS 17548684 #=INPUT-BASES 1263111136 #=INPUT-READS 17548684 #=MAPPED-BASES 1173670424 #=MAPPED-READS 16334798 SNP 1 4 NC_012967 1881721 T RA 2 . NC_012967 375729 0 T C bias_e_value=1.84014e-07 bias_p_value=3.97455e-14 consensus_reject=FREQUENCY_CUTOFF consensus_score=94.4 fisher_strand_p_value=1.18469e-15 frequency=4.553e-01 ks_quality_p_value=0.947089 major_base=T major_cov=25/42 major_frequency=5.447e-01 minor_base=C minor_cov=56/0 new_cov=56/0 polymorphism_frequency=4.553e-01 polymorphism_score=80.3 prediction=polymorphism ref_cov=25/42 total_cov=84/42 RA 3 . NC_012967 1459022 0 T G bias_e_value=51146.3 bias_p_value=0.0110472 consensus_reject=FREQUENCY_CUTOFF consensus_score=187.4 fisher_strand_p_value=0.00146833 frequency=2.500e-01 ks_quality_p_value=1 major_base=T major_cov=57/21 major_frequency=7.500e-01 minor_base=G minor_cov=26/0 new_cov=26/0 polymorphism_frequency=2.500e-01 polymorphism_score=11.6 prediction=polymorphism ref_cov=57/21 total_cov=83/21 RA 4 . NC_012967 1881721 0 G T bias_e_value=4402130 bias_p_value=0.950823 consensus_score=735.0 fisher_strand_p_value=1 frequency=1 ks_quality_p_value=0.703246 major_base=T major_cov=145/100 major_frequency=9.959e-01 minor_base=G minor_cov=1/0 new_cov=145/100 polymorphism_frequency=9.959e-01 polymorphism_score=-3.3 prediction=consensus ref_cov=1/0 total_cov=147/100 RA 5 . NC_012967 2016091 0 T A bias_e_value=117169 bias_p_value=0.0253075 consensus_reject=FREQUENCY_CUTOFF consensus_score=66.3 fisher_strand_p_value=0.00385948 frequency=3.191e-01 ks_quality_p_value=1 major_base=T major_cov=13/19 major_frequency=6.809e-01 minor_base=A minor_cov=0/15 new_cov=0/15 polymorphism_frequency=3.191e-01 polymorphism_score=26.7 prediction=polymorphism ref_cov=13/19 total_cov=13/34 RA 6 . NC_012967 2237486 0 G A bias_e_value=2415.14 bias_p_value=0.000521649 consensus_reject=FREQUENCY_CUTOFF consensus_score=129.2 fisher_strand_p_value=4.76303e-05 frequency=2.794e-01 ks_quality_p_value=1 major_base=G major_cov=24/25 major_frequency=7.206e-01 minor_base=A minor_cov=0/19 new_cov=0/19 polymorphism_frequency=2.794e-01 polymorphism_score=23.7 prediction=polymorphism ref_cov=24/25 total_cov=24/45 RA 7 . NC_012967 3174256 0 T G bias_e_value=2.59023e-08 bias_p_value=5.59468e-15 consensus_reject=FREQUENCY_CUTOFF consensus_score=249.7 fisher_strand_p_value=1.50176e-16 frequency=2.830e-01 ks_quality_p_value=0.995047 major_base=T major_cov=39/75 major_frequency=7.170e-01 minor_base=G minor_cov=45/0 new_cov=45/0 polymorphism_frequency=2.830e-01 polymorphism_score=41.4 prediction=polymorphism ref_cov=39/75 total_cov=84/75 RA 8 . NC_012967 3296372 1 . G bias_e_value=46325.8 bias_p_value=0.010006 consensus_reject=FREQUENCY_CUTOFF consensus_score=42.3 fisher_strand_p_value=0.00135449 frequency=2.500e-01 ks_quality_p_value=0.967216 major_base=. major_cov=2/13 major_frequency=7.500e-01 minor_base=G minor_cov=5/0 new_cov=5/0 polymorphism_frequency=2.500e-01 polymorphism_score=17.8 prediction=polymorphism ref_cov=2/13 total_cov=7/13 RA 9 . NC_012967 3823117 0 A C bias_e_value=12.6855 bias_p_value=2.73996e-06 consensus_reject=FREQUENCY_CUTOFF consensus_score=150.0 fisher_strand_p_value=1.64878e-07 frequency=2.619e-01 ks_quality_p_value=1 major_base=A major_cov=37/25 major_frequency=7.381e-01 minor_base=C minor_cov=0/22 new_cov=0/22 polymorphism_frequency=2.619e-01 polymorphism_score=17.6 prediction=polymorphism ref_cov=37/25 total_cov=37/48 MC 10 . NC_012967 3893603 3899626 1392 0 left_inside_cov=95 left_outside_cov=102 right_inside_cov=0 right_outside_cov=287 JC 11 . NC_012967 1 1 NC_012967 4629812 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=105 coverage_plus=131 flanking_left=72 flanking_right=72 frequency=1 junction_possible_overlap_registers=70 key=NC_012967__1__1__NC_012967__4629812__-1__0____72__72__0__0 max_left=71 max_left_minus=71 max_left_plus=71 max_min_left=35 max_min_left_minus=35 max_min_left_plus=35 max_min_right=36 max_min_right_minus=36 max_min_right_plus=35 max_pos_hash_score=142 max_right=71 max_right_minus=71 max_right_plus=71 neg_log10_pos_hash_p_value=0.1 new_junction_coverage=0.95 new_junction_read_count=239 polymorphism_frequency=1.000e+00 pos_hash_score=116 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=70 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=70 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=236 JC 12 . NC_012967 160632 1 NC_012967 326571 -1 0 alignment_overlap=7 coverage_minus=1 coverage_plus=3 flanking_left=72 flanking_right=72 frequency=1.416e-02 junction_possible_overlap_registers=63 key=NC_012967__160632__1__NC_012967__326578__-1__7____72__72__0__0 max_left=47 max_left_minus=47 max_left_plus=21 max_min_left=21 max_min_left_minus=0 max_min_left_plus=21 max_min_right=18 max_min_right_minus=18 max_min_right_plus=0 max_pos_hash_score=128 max_right=63 max_right_minus=18 max_right_plus=63 neg_log10_pos_hash_p_value=18.1 new_junction_coverage=0.02 new_junction_read_count=4 polymorphism_frequency=1.416e-02 pos_hash_score=4 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.43 side_1_overlap=7 side_1_possible_overlap_registers=70 side_1_read_count=359 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.04 side_2_overlap=0 side_2_possible_overlap_registers=63 side_2_read_count=234 side_2_redundant=0 total_non_overlap_reads=4 JC 13 . NC_012967 167449 1 NC_012967 1831654 -1 0 alignment_overlap=3 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=2.399e-02 junction_possible_overlap_registers=67 key=NC_012967__167449__1__NC_012967__1831657__-1__3____72__72__0__0 max_left=66 max_left_minus=66 max_left_plus=17 max_min_left=17 max_min_left_minus=17 max_min_left_plus=17 max_min_right=1 max_min_right_minus=1 max_min_right_plus=0 max_pos_hash_score=136 max_right=46 max_right_minus=46 max_right_plus=46 neg_log10_pos_hash_p_value=19.3 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=2.399e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.08 side_1_overlap=3 side_1_possible_overlap_registers=70 side_1_read_count=21 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.93 side_2_overlap=0 side_2_possible_overlap_registers=67 side_2_read_count=224 side_2_redundant=0 total_non_overlap_reads=3 JC 14 . NC_012967 252105 -1 NC_012967 743804 1 0 alignment_overlap=9 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.575e-02 junction_possible_overlap_registers=61 key=NC_012967__252105__-1__NC_012967__743795__1__9____72__72__0__0 max_left=54 max_left_minus=54 max_left_plus=18 max_min_left=18 max_min_left_minus=18 max_min_left_plus=18 max_min_right=7 max_min_right_minus=7 max_min_right_plus=0 max_pos_hash_score=124 max_right=39 max_right_minus=39 max_right_plus=39 neg_log10_pos_hash_p_value=18.6 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.575e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.84 side_1_overlap=9 side_1_possible_overlap_registers=70 side_1_read_count=210 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.88 side_2_overlap=0 side_2_possible_overlap_registers=61 side_2_read_count=192 side_2_redundant=0 total_non_overlap_reads=3 JC 15 . NC_012967 407457 1 NC_012967 2031550 -1 0 alignment_overlap=6 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.376e-02 junction_possible_overlap_registers=64 key=NC_012967__407457__1__NC_012967__2031556__-1__6____72__72__0__0 max_left=62 max_left_minus=62 max_left_plus=20 max_min_left=20 max_min_left_minus=0 max_min_left_plus=20 max_min_right=28 max_min_right_minus=28 max_min_right_plus=0 max_pos_hash_score=130 max_right=46 max_right_minus=28 max_right_plus=46 neg_log10_pos_hash_p_value=18.9 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.376e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.11 side_1_overlap=6 side_1_possible_overlap_registers=70 side_1_read_count=279 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.76 side_2_overlap=0 side_2_possible_overlap_registers=64 side_2_read_count=175 side_2_redundant=0 total_non_overlap_reads=3 JC 16 . NC_012967 480849 1 NC_012967 2293996 1 -11 alignment_overlap=-11 coverage_minus=7 coverage_plus=0 flanking_left=72 flanking_right=72 frequency=3.115e-01 junction_possible_overlap_registers=59 key=NC_012967__480849__1__NC_012967__2293996__1__-11__AGGGTGCGGGA__72__72__1__0 max_left=35 max_left_minus=35 max_left_plus=0 max_min_left=27 max_min_left_minus=27 max_min_left_plus=0 max_min_right=29 max_min_right_minus=29 max_min_right_plus=0 max_pos_hash_score=120 max_right=39 max_right_minus=39 max_right_plus=0 neg_log10_pos_hash_p_value=15.7 new_junction_coverage=0.25 new_junction_read_count=53 polymorphism_frequency=3.115e-01 pos_hash_score=7 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.56 side_2_overlap=0 side_2_possible_overlap_registers=70 side_2_read_count=139 side_2_redundant=0 total_non_overlap_reads=7 unique_read_sequence=AGGGTGCGGGA JC 17 . NC_012967 480950 1 NC_012967 2293996 1 -11 alignment_overlap=-11 coverage_minus=7 coverage_plus=0 flanking_left=72 flanking_right=72 frequency=3.392e-01 junction_possible_overlap_registers=59 key=NC_012967__480950__1__NC_012967__2293996__1__-11__AGGGTGCGGGA__72__72__0__0 max_left=35 max_left_minus=35 max_left_plus=0 max_min_left=27 max_min_left_minus=27 max_min_left_plus=0 max_min_right=29 max_min_right_minus=29 max_min_right_plus=0 max_pos_hash_score=120 max_right=39 max_right_minus=39 max_right_plus=0 neg_log10_pos_hash_p_value=15.7 new_junction_coverage=0.25 new_junction_read_count=53 polymorphism_frequency=3.392e-01 pos_hash_score=7 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.42 side_1_overlap=0 side_1_possible_overlap_registers=70 side_1_read_count=106 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.56 side_2_overlap=0 side_2_possible_overlap_registers=70 side_2_read_count=139 side_2_redundant=0 total_non_overlap_reads=7 unique_read_sequence=AGGGTGCGGGA JC 18 . NC_012967 602385 -1 NC_012967 1546703 1 0 alignment_overlap=12 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.267e-02 junction_possible_overlap_registers=58 key=NC_012967__602385__-1__NC_012967__1546691__1__12____72__72__0__0 max_left=59 max_left_minus=59 max_left_plus=17 max_min_left=17 max_min_left_minus=17 max_min_left_plus=17 max_min_right=1 max_min_right_minus=1 max_min_right_plus=0 max_pos_hash_score=118 max_right=24 max_right_minus=24 max_right_plus=24 neg_log10_pos_hash_p_value=18.2 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.267e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.27 side_1_overlap=12 side_1_possible_overlap_registers=70 side_1_read_count=318 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.98 side_2_overlap=0 side_2_possible_overlap_registers=58 side_2_read_count=204 side_2_redundant=0 total_non_overlap_reads=3 JC 19 . NC_012967 671435 -1 NC_012967 2066636 1 -10 alignment_overlap=-10 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=3.451e-01 junction_possible_overlap_registers=60 key=NC_012967__671435__-1__NC_012967__2066636__1__-10__TTTGTCACCA__72__72__0__0 max_left=38 max_left_minus=23 max_left_plus=38 max_min_left=23 max_min_left_minus=23 max_min_left_plus=0 max_min_right=25 max_min_right_minus=0 max_min_right_plus=25 max_pos_hash_score=122 max_right=43 max_right_minus=43 max_right_plus=25 neg_log10_pos_hash_p_value=18.5 new_junction_coverage=0.42 new_junction_read_count=91 polymorphism_frequency=3.451e-01 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.88 side_1_overlap=0 side_1_possible_overlap_registers=70 side_1_read_count=221 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.73 side_2_overlap=0 side_2_possible_overlap_registers=70 side_2_read_count=182 side_2_redundant=0 total_non_overlap_reads=3 unique_read_sequence=TTTGTCACCA JC 20 . NC_012967 880528 1 NC_012967 904682 -1 0 alignment_overlap=14 coverage_minus=25 coverage_plus=26 flanking_left=72 flanking_right=72 frequency=2.567e-01 junction_possible_overlap_registers=56 key=NC_012967__880528__1__NC_012967__904696__-1__14____72__72__0__0 max_left=57 max_left_minus=57 max_left_plus=52 max_min_left=28 max_min_left_minus=28 max_min_left_plus=25 max_min_right=29 max_min_right_minus=26 max_min_right_plus=29 max_pos_hash_score=114 max_right=57 max_right_minus=57 max_right_plus=57 neg_log10_pos_hash_p_value=5.7 new_junction_coverage=0.25 new_junction_read_count=51 polymorphism_frequency=2.567e-01 pos_hash_score=38 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.81 side_1_overlap=14 side_1_possible_overlap_registers=70 side_1_read_count=203 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.66 side_2_overlap=0 side_2_possible_overlap_registers=56 side_2_read_count=133 side_2_redundant=0 total_non_overlap_reads=51 JC 21 . NC_012967 943302 -1 NC_012967 943346 -1 0 alignment_overlap=5 coverage_minus=1 coverage_plus=2 flanking_left=72 flanking_right=72 frequency=1.290e-02 junction_possible_overlap_registers=65 key=NC_012967__943302__-1__NC_012967__943351__-1__5____72__72__0__0 max_left=29 max_left_minus=22 max_left_plus=29 max_min_left=29 max_min_left_minus=22 max_min_left_plus=29 max_min_right=0 max_min_right_minus=0 max_min_right_plus=0 max_pos_hash_score=132 max_right=40 max_right_minus=40 max_right_plus=40 neg_log10_pos_hash_p_value=19.1 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.290e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.01 side_1_overlap=5 side_1_possible_overlap_registers=70 side_1_read_count=252 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.97 side_2_overlap=0 side_2_possible_overlap_registers=65 side_2_read_count=225 side_2_redundant=0 total_non_overlap_reads=3 JC 22 . NC_012967 1175409 1 NC_012967 4111506 -1 0 alignment_overlap=6 coverage_minus=1 coverage_plus=2 flanking_left=72 flanking_right=72 frequency=1.130e-02 junction_possible_overlap_registers=64 key=NC_012967__1175409__1__NC_012967__4111512__-1__6____72__72__0__0 max_left=25 max_left_minus=25 max_left_plus=25 max_min_left=25 max_min_left_minus=25 max_min_left_plus=25 max_min_right=0 max_min_right_minus=0 max_min_right_plus=0 max_pos_hash_score=130 max_right=65 max_right_minus=26 max_right_plus=65 neg_log10_pos_hash_p_value=18.9 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.130e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.07 side_1_overlap=6 side_1_possible_overlap_registers=70 side_1_read_count=267 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.23 side_2_overlap=0 side_2_possible_overlap_registers=64 side_2_read_count=281 side_2_redundant=0 total_non_overlap_reads=3 JC 23 . NC_012967 1589809 -1 NC_012967 4271600 1 0 alignment_overlap=5 coverage_minus=1 coverage_plus=2 flanking_left=72 flanking_right=72 frequency=1.265e-02 junction_possible_overlap_registers=65 key=NC_012967__1589809__-1__NC_012967__4271595__1__5____72__72__0__0 max_left=22 max_left_minus=22 max_left_plus=22 max_min_left=22 max_min_left_minus=22 max_min_left_plus=22 max_min_right=0 max_min_right_minus=0 max_min_right_plus=0 max_pos_hash_score=132 max_right=66 max_right_minus=23 max_right_plus=66 neg_log10_pos_hash_p_value=19.1 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.265e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.11 side_1_overlap=5 side_1_possible_overlap_registers=70 side_1_read_count=278 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.90 side_2_overlap=0 side_2_possible_overlap_registers=65 side_2_read_count=210 side_2_redundant=0 total_non_overlap_reads=3 JC 24 . NC_012967 1807533 -1 NC_012967 4242016 -1 0 alignment_overlap=5 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.255e-02 junction_possible_overlap_registers=65 key=NC_012967__1807533__-1__NC_012967__4242021__-1__5____72__72__0__0 max_left=64 max_left_minus=64 max_left_plus=22 max_min_left=22 max_min_left_minus=0 max_min_left_plus=22 max_min_right=31 max_min_right_minus=31 max_min_right_plus=0 max_pos_hash_score=132 max_right=45 max_right_minus=31 max_right_plus=45 neg_log10_pos_hash_p_value=19.1 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.255e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.05 side_1_overlap=5 side_1_possible_overlap_registers=70 side_1_read_count=263 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.98 side_2_overlap=0 side_2_possible_overlap_registers=65 side_2_read_count=228 side_2_redundant=0 total_non_overlap_reads=3 JC 25 . NC_012967 1830600 -1 NC_012967 2821771 1 0 alignment_overlap=8 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.352e-02 junction_possible_overlap_registers=62 key=NC_012967__1830600__-1__NC_012967__2821763__1__8____72__72__0__0 max_left=22 max_left_minus=22 max_left_plus=22 max_min_left=1 max_min_left_minus=1 max_min_left_plus=0 max_min_right=13 max_min_right_minus=13 max_min_right_plus=13 max_pos_hash_score=126 max_right=63 max_right_minus=63 max_right_plus=13 neg_log10_pos_hash_p_value=18.7 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.352e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.85 side_1_overlap=8 side_1_possible_overlap_registers=70 side_1_read_count=212 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.13 side_2_overlap=0 side_2_possible_overlap_registers=62 side_2_read_count=250 side_2_redundant=0 total_non_overlap_reads=3 JC 26 . NC_012967 1983149 1 NC_012967 1983274 1 0 alignment_overlap=6 coverage_minus=1 coverage_plus=2 flanking_left=72 flanking_right=72 frequency=1.540e-02 junction_possible_overlap_registers=64 key=NC_012967__1983149__1__NC_012967__1983268__1__6____72__72__0__0 max_left=43 max_left_minus=43 max_left_plus=28 max_min_left=28 max_min_left_minus=0 max_min_left_plus=28 max_min_right=23 max_min_right_minus=23 max_min_right_plus=0 max_pos_hash_score=130 max_right=63 max_right_minus=23 max_right_plus=63 neg_log10_pos_hash_p_value=18.9 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.540e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.90 side_1_overlap=6 side_1_possible_overlap_registers=70 side_1_read_count=225 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.78 side_2_overlap=0 side_2_possible_overlap_registers=64 side_2_read_count=178 side_2_redundant=0 total_non_overlap_reads=3 JC 27 . NC_012967 2045389 1 NC_012967 2045582 1 0 alignment_overlap=8 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.523e-02 junction_possible_overlap_registers=62 key=NC_012967__2045389__1__NC_012967__2045574__1__8____72__72__0__0 max_left=47 max_left_minus=47 max_left_plus=27 max_min_left=27 max_min_left_minus=0 max_min_left_plus=27 max_min_right=22 max_min_right_minus=22 max_min_right_plus=0 max_pos_hash_score=126 max_right=37 max_right_minus=22 max_right_plus=37 neg_log10_pos_hash_p_value=18.7 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.523e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.91 side_1_overlap=8 side_1_possible_overlap_registers=70 side_1_read_count=227 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.84 side_2_overlap=0 side_2_possible_overlap_registers=62 side_2_read_count=187 side_2_redundant=0 total_non_overlap_reads=3 JC 28 . NC_012967 2066637 1 NC_012967 4208344 -1 -12 alignment_overlap=-12 coverage_minus=4 coverage_plus=3 flanking_left=72 flanking_right=72 frequency=2.196e-01 junction_possible_overlap_registers=58 key=NC_012967__2066637__1__NC_012967__4208344__-1__-12__GTTGGCGCACAA__72__72__0__0 max_left=37 max_left_minus=37 max_left_plus=23 max_min_left=28 max_min_left_minus=28 max_min_left_plus=23 max_min_right=21 max_min_right_minus=21 max_min_right_plus=0 max_pos_hash_score=118 max_right=37 max_right_minus=32 max_right_plus=37 neg_log10_pos_hash_p_value=15.6 new_junction_coverage=0.18 new_junction_read_count=38 polymorphism_frequency=2.196e-01 pos_hash_score=7 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.72 side_1_overlap=0 side_1_possible_overlap_registers=70 side_1_read_count=181 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.58 side_2_overlap=0 side_2_possible_overlap_registers=70 side_2_read_count=145 side_2_redundant=0 total_non_overlap_reads=7 unique_read_sequence=GTTGGCGCACAA JC 29 . NC_012967 2289885 1 NC_012967 2290097 1 0 alignment_overlap=4 coverage_minus=1 coverage_plus=2 flanking_left=72 flanking_right=72 frequency=1.355e-02 junction_possible_overlap_registers=66 key=NC_012967__2289885__1__NC_012967__2290093__1__4____72__72__0__0 max_left=23 max_left_minus=23 max_left_plus=23 max_min_left=2 max_min_left_minus=0 max_min_left_plus=2 max_min_right=17 max_min_right_minus=17 max_min_right_plus=17 max_pos_hash_score=134 max_right=64 max_right_minus=17 max_right_plus=64 neg_log10_pos_hash_p_value=19.2 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.355e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.91 side_1_overlap=4 side_1_possible_overlap_registers=70 side_1_read_count=229 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.94 side_2_overlap=0 side_2_possible_overlap_registers=66 side_2_read_count=221 side_2_redundant=0 total_non_overlap_reads=3 JC 30 . NC_012967 2334542 1 NC_012967 2452488 1 0 alignment_overlap=5 coverage_minus=1 coverage_plus=2 flanking_left=72 flanking_right=72 frequency=1.173e-02 junction_possible_overlap_registers=65 key=NC_012967__2334542__1__NC_012967__2452483__1__5____72__72__0__0 max_left=47 max_left_minus=47 max_left_plus=37 max_min_left=1 max_min_left_minus=0 max_min_left_plus=1 max_min_right=30 max_min_right_minus=20 max_min_right_plus=30 max_pos_hash_score=132 max_right=66 max_right_minus=20 max_right_plus=66 neg_log10_pos_hash_p_value=19.1 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.173e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.08 side_1_overlap=5 side_1_possible_overlap_registers=70 side_1_read_count=270 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.10 side_2_overlap=0 side_2_possible_overlap_registers=65 side_2_read_count=255 side_2_redundant=0 total_non_overlap_reads=3 JC 31 . NC_012967 2527115 1 NC_012967 4020488 -1 0 alignment_overlap=7 coverage_minus=1 coverage_plus=4 flanking_left=72 flanking_right=72 frequency=1.903e-02 junction_possible_overlap_registers=63 key=NC_012967__2527115__1__NC_012967__4020495__-1__7____72__72__0__0 max_left=36 max_left_minus=36 max_left_plus=36 max_min_left=1 max_min_left_minus=0 max_min_left_plus=1 max_min_right=24 max_min_right_minus=24 max_min_right_plus=24 max_pos_hash_score=128 max_right=64 max_right_minus=24 max_right_plus=64 neg_log10_pos_hash_p_value=17.4 new_junction_coverage=0.02 new_junction_read_count=5 polymorphism_frequency=1.903e-02 pos_hash_score=5 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.18 side_1_overlap=7 side_1_possible_overlap_registers=70 side_1_read_count=296 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.11 side_2_overlap=0 side_2_possible_overlap_registers=63 side_2_read_count=249 side_2_redundant=0 total_non_overlap_reads=5 JC 32 . NC_012967 2838593 1 NC_012967 3130814 1 0 alignment_overlap=9 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.643e-02 junction_possible_overlap_registers=61 key=NC_012967__2838593__1__NC_012967__3130805__1__9____72__72__0__0 max_left=62 max_left_minus=62 max_left_plus=38 max_min_left=0 max_min_left_minus=0 max_min_left_plus=0 max_min_right=22 max_min_right_minus=22 max_min_right_plus=22 max_pos_hash_score=124 max_right=22 max_right_minus=22 max_right_plus=22 neg_log10_pos_hash_p_value=18.6 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.643e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.08 side_1_overlap=9 side_1_possible_overlap_registers=70 side_1_read_count=271 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.56 side_2_overlap=0 side_2_possible_overlap_registers=61 side_2_read_count=123 side_2_redundant=0 total_non_overlap_reads=3 JC 33 . NC_012967 3131687 -1 NC_012967 4502277 -1 0 alignment_overlap=2 coverage_minus=1 coverage_plus=2 flanking_left=72 flanking_right=72 frequency=1.056e-02 junction_possible_overlap_registers=68 key=NC_012967__3131687__-1__NC_012967__4502279__-1__2____72__72__0__0 max_left=23 max_left_minus=23 max_left_plus=23 max_min_left=23 max_min_left_minus=23 max_min_left_plus=23 max_min_right=0 max_min_right_minus=0 max_min_right_plus=0 max_pos_hash_score=138 max_right=62 max_right_minus=25 max_right_plus=62 neg_log10_pos_hash_p_value=19.4 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.056e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.10 side_1_overlap=2 side_1_possible_overlap_registers=70 side_1_read_count=275 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.21 side_2_overlap=0 side_2_possible_overlap_registers=68 side_2_read_count=295 side_2_redundant=0 total_non_overlap_reads=3 JC 34 . NC_012967 3419219 -1 NC_012967 3596233 1 0 alignment_overlap=8 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.179e-02 junction_possible_overlap_registers=62 key=NC_012967__3419219__-1__NC_012967__3596225__1__8____72__72__0__1 max_left=56 max_left_minus=56 max_left_plus=28 max_min_left=0 max_min_left_minus=0 max_min_left_plus=0 max_min_right=13 max_min_right_minus=13 max_min_right_plus=13 max_pos_hash_score=126 max_right=13 max_right_minus=13 max_right_plus=13 neg_log10_pos_hash_p_value=18.7 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.179e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.13 side_1_overlap=8 side_1_possible_overlap_registers=70 side_1_read_count=284 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=1 total_non_overlap_reads=3 JC 35 . NC_012967 3462190 -1 NC_012967 4348367 -1 0 alignment_overlap=8 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=1.076e-02 junction_possible_overlap_registers=62 key=NC_012967__3462190__-1__NC_012967__4348375__-1__8____72__72__0__0 max_left=60 max_left_minus=60 max_left_plus=30 max_min_left=30 max_min_left_minus=0 max_min_left_plus=30 max_min_right=19 max_min_right_minus=19 max_min_right_plus=0 max_pos_hash_score=126 max_right=34 max_right_minus=19 max_right_plus=34 neg_log10_pos_hash_p_value=18.7 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=1.076e-02 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.41 side_1_overlap=8 side_1_possible_overlap_registers=70 side_1_read_count=353 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.08 side_2_overlap=0 side_2_possible_overlap_registers=62 side_2_read_count=239 side_2_redundant=0 total_non_overlap_reads=3 JC 36 . NC_012967 3482676 1 NC_012967 3482700 -1 0 alignment_overlap=6 coverage_minus=20 coverage_plus=43 flanking_left=72 flanking_right=72 frequency=4.686e-01 junction_possible_overlap_registers=64 key=NC_012967__3482676__1__NC_012967__3482706__-1__6____72__72__0__0 max_left=65 max_left_minus=64 max_left_plus=65 max_min_left=19 max_min_left_minus=19 max_min_left_plus=15 max_min_right=33 max_min_right_minus=23 max_min_right_plus=33 max_pos_hash_score=130 max_right=65 max_right_minus=65 max_right_plus=65 neg_log10_pos_hash_p_value=6.8 new_junction_coverage=0.30 new_junction_read_count=68 polymorphism_frequency=4.686e-01 pos_hash_score=38 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.46 side_1_overlap=6 side_1_possible_overlap_registers=70 side_1_read_count=114 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.22 side_2_overlap=0 side_2_possible_overlap_registers=64 side_2_read_count=50 side_2_redundant=0 total_non_overlap_reads=63 JC 37 . NC_012967 3482701 1 NC_012967 3482706 -1 -19 alignment_overlap=-19 coverage_minus=0 coverage_plus=9 flanking_left=72 flanking_right=72 frequency=2.031e-01 junction_possible_overlap_registers=51 key=NC_012967__3482701__1__NC_012967__3482706__-1__-19__CCCGCCGCCAGTTCCCACT__72__72__0__0 max_left=33 max_left_minus=0 max_left_plus=33 max_min_left=24 max_min_left_minus=0 max_min_left_plus=24 max_min_right=26 max_min_right_minus=0 max_min_right_plus=26 max_pos_hash_score=104 max_right=52 max_right_minus=0 max_right_plus=52 neg_log10_pos_hash_p_value=14.5 new_junction_coverage=0.07 new_junction_read_count=13 polymorphism_frequency=2.031e-01 pos_hash_score=7 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.31 side_1_overlap=0 side_1_possible_overlap_registers=70 side_1_read_count=77 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.25 side_2_overlap=0 side_2_possible_overlap_registers=70 side_2_read_count=63 side_2_redundant=0 total_non_overlap_reads=9 unique_read_sequence=CCCGCCGCCAGTTCCCACT JC 38 . NC_012967 3482704 1 NC_012967 3482706 -1 -22 alignment_overlap=-22 coverage_minus=0 coverage_plus=5 flanking_left=72 flanking_right=72 frequency=1.133e-01 junction_possible_overlap_registers=48 key=NC_012967__3482704__1__NC_012967__3482706__-1__-22__CGCTCCGCCGCCAGTTCCCACT__72__72__0__0 max_left=22 max_left_minus=0 max_left_plus=22 max_min_left=22 max_min_left_minus=0 max_min_left_plus=22 max_min_right=0 max_min_right_minus=0 max_min_right_plus=0 max_pos_hash_score=98 max_right=46 max_right_minus=0 max_right_plus=46 neg_log10_pos_hash_p_value=16.0 new_junction_coverage=0.03 new_junction_read_count=6 polymorphism_frequency=1.133e-01 pos_hash_score=4 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.30 side_1_overlap=0 side_1_possible_overlap_registers=70 side_1_read_count=74 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.25 side_2_overlap=0 side_2_possible_overlap_registers=70 side_2_read_count=63 side_2_redundant=0 total_non_overlap_reads=5 unique_read_sequence=CGCTCCGCCGCCAGTTCCCACT JC 39 . NC_012967 3634909 1 NC_012967 4237813 1 0 alignment_overlap=3 coverage_minus=2 coverage_plus=1 flanking_left=72 flanking_right=72 frequency=9.436e-03 junction_possible_overlap_registers=67 key=NC_012967__3634909__1__NC_012967__4237810__1__3____72__72__0__0 max_left=67 max_left_minus=67 max_left_plus=27 max_min_left=34 max_min_left_minus=34 max_min_left_plus=27 max_min_right=2 max_min_right_minus=2 max_min_right_plus=0 max_pos_hash_score=136 max_right=42 max_right_minus=35 max_right_plus=42 neg_log10_pos_hash_p_value=19.3 new_junction_coverage=0.01 new_junction_read_count=3 polymorphism_frequency=9.436e-03 pos_hash_score=3 prediction=polymorphism reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=1.50 side_1_overlap=3 side_1_possible_overlap_registers=70 side_1_read_count=376 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.13 side_2_overlap=0 side_2_possible_overlap_registers=67 side_2_read_count=270 side_2_redundant=0 total_non_overlap_reads=3 JC 40 . NC_012967 3894995 -1 NC_012967 3899627 1 0 alignment_overlap=1 coverage_minus=140 coverage_plus=104 flanking_left=72 flanking_right=72 frequency=1 junction_possible_overlap_registers=69 key=NC_012967__3894996__-1__NC_012967__3899627__1__1____72__72__1__0 max_left=68 max_left_minus=68 max_left_plus=68 max_min_left=35 max_min_left_minus=35 max_min_left_plus=34 max_min_right=35 max_min_right_minus=35 max_min_right_plus=35 max_pos_hash_score=140 max_right=70 max_right_minus=69 max_right_plus=70 neg_log10_pos_hash_p_value=0.1 new_junction_coverage=1.09 new_junction_read_count=268 polymorphism_frequency=1.000e+00 pos_hash_score=113 prediction=consensus side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=1 side_2_possible_overlap_registers=70 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=244 UN 41 . 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