New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1623544	27 (0.580)	4 (0.090)	3/238	NT	13.4%	intergenic (+29/+54)	marA/malL	Multiple antibiotic resistance protein MarA/Oligo‑1,6‑glucosidase
	?	USA300TCH1516_ALE	= 1623575	27 (0.640)					intergenic (+60/+23)	marA/malL	Multiple antibiotic resistance protein MarA/Oligo‑1,6‑glucosidase

TTATATGTTGAAGTGTACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCC  >  USA300TCH1516_ALE/1623414‑1623684                                                                                                                                   |                                                                                                                                             ttATATGTTGAAGTGTACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAgg                                                                                                                                    <  2:207364/141‑1 (MQ=255)  tataTGTTGAAGTGTACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGt                                                                                                                                   >  1:596420/1‑141 (MQ=255)       gTTGAAGTGTACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACa                                                                                                                              <  1:386981/141‑1 (MQ=255)        ttGAAGTGTACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACaa                                                                                                                             <  2:15481/141‑1 (MQ=255)            aGTGTACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATgg                                                                                                                         <  1:198033/141‑1 (MQ=255)             gtgtACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGc                                                                                                                        <  1:185198/141‑1 (MQ=255)               gtACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCt                                                                                                                      <  1:619333/141‑1 (MQ=255)                     tctcGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATAgaatctaaggccatttgtagacctatagat                                                                                                                <  2:106515‑M1/141‑31 (MQ=255)                       tcGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATAgaatctaaggccatttgtagacctatagatat                                                                                                              <  1:678068‑M1/141‑33 (MQ=255)                       tcGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATAgaatctaaggccatttgtagacctatagatat                                                                                                              <  1:603622‑M1/141‑33 (MQ=255)                       tCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCt                                                                                                              <  2:252612‑M2/141‑2 (MQ=255)                            atTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCtattag                                                                                                         <  1:217897‑M2/141‑7 (MQ=255)                            atTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCtattag                                                                                                         <  1:745138‑M2/141‑7 (MQ=255)                              ttCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCtattaggg                                                                                                       >  1:549011‑M2/1‑133 (MQ=255)                               tCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATAgaatctaaggccatttgtagacctatagatatattagggg                                                                                                      <  1:122543‑M1/141‑41 (MQ=255)                                          cccATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAACAAAGAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAata                                                                                           >  1:574570/1‑141 (MQ=255)                                                 aCTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAAt                                                                                    >  1:397490/1‑141 (MQ=255)                                                  cTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAAtt                                                                                   >  1:244871/1‑141 (MQ=255)                                                  cTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAAtt                                                                                   <  1:616172/141‑1 (MQ=255)                                                             cTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATaa                                                                        <  1:454948/141‑1 (MQ=255)                                                             cTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATaa                                                                        <  1:108255/141‑1 (MQ=255)                                                                tGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAacac                                                                     >  1:570288/1‑141 (MQ=255)                                                                  gATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACAt                                                                   <  1:549791/141‑1 (MQ=255)                                                                      ccTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCtt                                                               <  2:53566/141‑1 (MQ=255)                                                                       cTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTc                                                              >  2:275265/1‑141 (MQ=255)                                                                                 gagTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGt                                                    >  1:375062/1‑141 (MQ=255)                                                                                            aCGAAGATTAAAGAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTaa                                         <  1:702709/141‑1 (MQ=255)                                                                                                     aaaTAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACttt                                >  1:375997/1‑141 (MQ=255)                                                                                                       ataataAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTgg                              >  1:147929/1‑141 (MQ=255)                                                                                                        taataaAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGc                             <  1:345596/141‑1 (MQ=255)                                                                                                               aaaCAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATaa                      <  1:720930/141‑1 (MQ=255)                                                                                                                          cccccTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCtt           <  2:100367/141‑1 (MQ=255)                                                                                                                           ccccTAATATATCTATAGGTCTACAAATGGCCTTAGATTCtattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatga          <  1:122543‑M2/141‑102 (MQ=255)                                                                                                                            cccTAATAgaatctaaggccatttgtagacctatagatatattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaa         >  1:549011‑M1/1‑8 (MQ=255)                                                                                                                            cccTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTa         >  1:615309/1‑141 (MQ=255)                                                                                                                              cTAATAgaatctaaggccatttgtagacctatagatatattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaat       <  1:745138‑M1/141‑136 (MQ=255)                                                                                                                              cTAATAgaatctaaggccatttgtagacctatagatatattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaat       <  1:217897‑M1/141‑136 (MQ=255)                                                                                                                              cTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACt       <  2:145418/141‑1 (MQ=255)                                                                                                                              cTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACt       <  1:665374/141‑1 (MQ=255)                                                                                                                                aaTATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTtc     <  2:148373/141‑1 (MQ=255)                                                                                                                                   atatCTATAGGTCTACAAATGGCCTTAGATTCtattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaatatcga  <  1:678068‑M2/141‑110 (MQ=255)                                                                                                                                   atatCTATAGGTCTACAAATGGCCTTAGATTCtattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaatatcga  <  1:603622‑M2/141‑110 (MQ=255)                                                                                                                                   atatCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTcc  >  1:572811/1‑141 (MQ=255)                                                                                                                                   agaatctaaggccatttgtagacctatagatatattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaatatcga  <  2:252612‑M1/141‑141 (MQ=255)                                                                                                                                   |                                                                                                                                             TTATATGTTGAAGTGTACCCTCTCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCC  >  USA300TCH1516_ALE/1623414‑1623684

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.