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

TCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTAATTCT  >  USA300TCH1516_ALE/1623436‑1623715                                                                                                                                            |                                                                                                                                             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)                    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                                                                                                       <  1:108255/141‑1 (MQ=255)                                       cTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATaa                                                                                                       <  1:454948/141‑1 (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)                                                                                                      cccTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTa                                        >  1:615309/1‑141 (MQ=255)                                                                                                        cTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACt                                      <  2:145418/141‑1 (MQ=255)                                                                                                        cTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACt                                      <  1:665374/141‑1 (MQ=255)                                                                                                          aaTATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTtc                                    <  2:148373/141‑1 (MQ=255)                                                                                                             atatCTATAGGTCTACAAATGGCCTTAGATTCtattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaatatcga                                 <  1:603622‑M2/141‑110 (MQ=255)                                                                                                             atatCTATAGGTCTACAAATGGCCTTAGATTCtattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaatatcga                                 <  1:678068‑M2/141‑110 (MQ=255)                                                                                                             atatCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTcc                                 >  1:572811/1‑141 (MQ=255)                                                                                                               atCTATAGGTCTACAAATGGCCTTAGATTCtattagggggcttctttgttttttattatttaatcttcgtcataaggactctgtttaacaggaatccaaagctgaattttagtgaatgggtcattaaatgaaatatcgaga                               <  2:106515‑M2/141‑112 (MQ=255)                                                                                                               atCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCAt                               >  2:41000/1‑141 (MQ=255)                                                                                                                     aGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTa                         <  1:264504/141‑1 (MQ=255)                                                                                                                                tGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGt              >  2:90616/1‑141 (MQ=255)                                                                                                                                      tAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGtt        >  1:70477/1‑141 (MQ=255)                                                                                                                                      tAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGtt        >  2:258876/1‑141 (MQ=255)                                                                                                                                        gATTCTATTAGGGGGCATATTAATATGTTCATTTAGTTCGATAACCCATGCTCACTCTCGACGTACCTGTCTTACTTTACCTTTTGCAGCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTaa      <  2:114022/141‑1 (MQ=255)                                                                                                                                        gATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTaa      <  1:218434/141‑1 (MQ=255)                                                                                                                                          ttCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTAAtt    <  1:518844/141‑1 (MQ=255)                                                                                                                                          ttCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTAAtt    <  1:276361/141‑1 (MQ=255)                                                                                                                                           tCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTAATTc   <  1:142279/141‑1 (MQ=255)                                                                                                                                            cTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTAATTCt  >  1:763385/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                             TCGATATTTCATTTAATGACCCATTCACTAAAATTCAGCTTTGGATTCCTGTTAAACAGAGTCCTTATGACGAAGATTAAATAATAAAAAACAAAGAAGCCCCCTAATATATCTATAGGTCTACAAATGGCCTTAGATTCTATTAGGGGGCATATTAATATGTTAATTTAGTTCGATAACACATGCTTCATATGGACGTAACTGTTTTAAATTAACTTTGGCATCATAATTAAATAGCTTTACTTCTCCATGGCTTAAATCAAATGGTACAGTTAATTCT  >  USA300TCH1516_ALE/1623436‑1623715

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.