Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	568,268	IS1 (–) +9 bp	intergenic (+21/‑39)	renD → / → emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	19796 =	NA (NA)	53 (0.840)	46/282	0.3	98.0%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	= 568276	1 (0.020)					intergenic (+29/‑39)	renD/emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
*	?	NC_000913	= 258675	NA (NA)	51 (0.800)	40/284	0.6	98.0%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	568268 =	1 (0.020)					intergenic (+21/‑47)	renD/emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE

CTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258537‑258675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGGTTATG  >  NC_000913/568268‑568406                                                                                                                                                                                                                                                                                        CTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAA                                                                                                                                         >  1:196281/1‑143  TGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACCGATGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGACTCGCCCAAAC                                                                                                                                        >  2:847661/1‑143                  TTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCT                                                                                                                        >  2:674009/1‑143                  TTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTAGAGCACCTCAAAAACACCAACATACACTAAATCAGTAAGTTGACAGCATCACCCAAACTGTAGTACAATTGTCT                                                                                                                        >  2:153021/1‑143                   TTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACCCTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTC                                                                                                                       >  1:230568/1‑143                   TTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAAGAGAGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATAAGTATGATGGCAGCAACACCCAAACTGAAGTACAATTCTCTC                                                                                                                       >  2:243660/1‑143                       CCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGT                                                                                                                   <  1:617253/143‑1                          TTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACACTGTGCGAGGAATTCAGGAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTG                                                                                                                >  1:835248/1‑143                            ACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAA                                                                                                              <  2:525971/143‑1                                ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGG                                                                                                          >  2:416212/1‑143                                ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGG                                                                                                          >  2:292178/1‑143                                  ccgCCCGACAGTAGCTGAAGAGGAGGGAGAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCAGCCAAACTGTAGTACAATGCTCTCCAGTTTGAACAGGAA                                                                                                        <  2:181228/140‑1                                   ACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGTCTTGGGATCACCTCACAAACACCATCATACACTAACTCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAA                                                                                                       <  1:715946/143‑1                                   ACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAA                                                                                                       <  1:439916/143‑1                                     CCCGTCAGTAGCTGAACAGGAGGGGCAGCTGATAGAAACAGAAGCCACTGGAGCACCTC‑AAAACACCATCATACACTCAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGCACAGGAAAGAA                                                                                                    >  1:157369/1‑143                                           gGTAGCTGAGCAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGC                                                                                               <  2:414773/142‑1                                           AGTACCTTAACAGGAGGGACAGTTGATAGAAACCGAACCCACTGGAGCCCCTCAAAAACACCATCATCCACGAAATCATTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCGCTCCAGTTTGAACAGGAAAGAATATGC                                                                                               <  2:962902/143‑1                                            GTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCT                                                                                              <  1:131781/143‑1                                                 TGAACAGAGGGGAAAGCTTATAGAAACAGAAGCCACTGGAGCAGCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTATTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAA                                                                                         <  2:755219/143‑1                                                    ACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTCACCCGGAAAGAATATGCTATGAACCC                                                                                      >  1:33901/1‑143                                                        GAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGCACAGGGAAGAATATGCTATGAACCCTTAT                                                                                  >  1:117548/1‑143                                                            GACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTT                                                                              >  2:98259/1‑143                                                              CAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTAT                                                                            <  1:292178/143‑1                                                                GCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCTGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCT                                                                          >  2:571856/1‑143                                                                    ATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCCGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGACAGAATATGCTATGAACCCTTATACTTATCTTGGc                                                                      >  1:253428/1‑142                                                                    ATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTAACTTGGT                                                                      >  1:14031/1‑143                                                                     gAGAAACAGAAGGCACTGGAGCACATCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTG                                                                     <  2:525390/142‑1                                                                       GAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGT                                                                   >  1:230417/1‑143                                                                          ACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCCGTTCCAGCAGGAAAGAACATACTTTGAACCCTTATATTTATCTTGGTGGTGCA                                                                >  2:550408/1‑143                                                                          ACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCA                                                                >  1:77681/1‑143                                                                                 CCACTGGAGCACCTCAAAAACACCATCATACACTACATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTG                                                         <  1:40415/143‑1                                                                                 CCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATCTTTATCCTGGTAGTGCAATACTTG                                                         >  2:477421/1‑143                                                                                 CCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTcg                                                         >  2:1087918/1‑141                                                                                 CCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTCATCTTGGTGGTGCAATACTTG                                                         >  1:607740/1‑143                                                                                              TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGG                                            >  1:805613/1‑143                                                                                              TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGG                                            >  1:1007885/1‑143                                                                                                      ACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCCATACTTGCAGAGGTCATTGGTACAACCT                                    >  1:199664/1‑143                                                                                                        CATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTA                                  >  1:1041279/1‑143                                                                                                         ATCATACAGTAAATCAGTAAGTTGGCAGCATAACCCAAACTGTAGTACAATTCTCCCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAA                                 <  1:63900/143‑1                                                                                                             agCACTAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCCTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAA                             <  2:984963/141‑1                                                                                                                  TAAATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGCAGTTTT                        >  1:94000/1‑143                                                                                                                   aacTCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCCTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTC                       <  1:431422/140‑1                                                                                                                     ATCAGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCACTACTTGCAGCGCTCATTGGTACACCCTTAATGAAGTTTTCgg                     >  2:1101795/1‑141                                                                                                                        AGTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGAATAATAACGTCAGATGTCATTGGTACAACCTTAATGAAGTTTTCAGAAG                  >  2:808141/1‑143                                                                                                                         GTAAGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGG                 <  1:571856/143‑1                                                                                                                            AGTTGGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTT              <  1:674009/143‑1                                                                                                                                GGCAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCGGAAGGTTTTACA          >  2:233167/1‑143                                                                                                                                  CAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTCATGAAGTTTTCAGAAGGTTTTACACG        >  1:408205/1‑143                                                                                                                                  CAGCATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACG        <  1:243839/143‑1                                                                                                                                     CATCACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGGTT     >  2:330742/1‑143                                                                                                                                        CACCCAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGGTTATG  <  1:416212/143‑1                                                                                                                                                                                                                                                                                        CTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258537‑258675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAAACTGTAGTACAATTCTCTCCAGTTTGAACAGGAAAGAATATGCTATGAACCCTTATATTTATCTTGGTGGTGCAATACTTGCAGAGGTCATTGGTACAACCTTAATGAAGTTTTCAGAAGGTTTTACACGGTTATG  >  NC_000913/568268‑568406

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.