New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 705329	36 (1.040)	3 (0.090)	3/242	NT	7.6%	intergenic (+1079/+81)	nhaK_1/mntA	Sodium, potassium, lithium and rubidium/H(+) antiporter/Manganese‑binding lipoprotein MntA
	?	USA300TCH1516_ALE	= 705368	39 (1.210)					intergenic (+1118/+42)	nhaK_1/mntA	Sodium, potassium, lithium and rubidium/H(+) antiporter/Manganese‑binding lipoprotein MntA

GCTTTTCTCTTTCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTTCATCATTTTGTAGTAAGAGT  >  USA300TCH1516_ALE/705192‑705468                                                                                                                                          |                                                                                                                                            gCTTTTCTCTTTCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGAATTTGTTATGTTGAtgtgt                                                                                                                                          >  1:25882/1‑141 (MQ=255)     ttCTCTTTCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGcc                                                                                                                                      <  1:108482/141‑1 (MQ=255)        tctTTCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTaa                                                                                                                                   <  1:213201/141‑1 (MQ=255)           ttgaacgaaaGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAat                                                                                                                                >  1:104544/8‑141 (MQ=255)            tCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGcaacctaaaatatt                                                                                                                               >  2:29207‑M1/1‑127 (MQ=255)                     aagaAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATa                                                                                                                      <  1:10342/140‑1 (MQ=255)                        aaGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCa                                                                                                                   <  2:246699/141‑1 (MQ=255)                         aGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCaa                                                                                                                  <  2:263514/141‑1 (MQ=255)                           ttCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAata                                                                                                                <  1:138425/141‑1 (MQ=255)                           ttCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGCAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAata                                                                                                                <  2:175030/141‑1 (MQ=255)                                     acgctagcGTGCGATCGCGAATGGTATATATATTAATAGGAGTGTAATATATATTGAACTAACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTg                                                                                                      <  2:370624/134‑1 (MQ=255)                                         tatCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGTCTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAATATATTGGAGATACCAATATTTTAGGTTGcatc                                                                                                  >  2:379197‑M2/1‑137 (MQ=255)                                          atCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGcatca                                                                                                 <  2:393864‑M2/141‑6 (MQ=255)                                           tCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGcatcaa                                                                                                <  2:397555‑M2/141‑7 (MQ=255)                                            cGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGcaacctaaaatattggtatctccaatattttaggccacacatcaac                                                                                               <  1:29207‑M1/141‑47 (MQ=255)                                            cGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGcatcaac                                                                                               <  2:305529‑M2/141‑8 (MQ=255)                                              ttctatcggGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGcatcaacat                                                                                             >  2:310260‑M2/5‑132 (MQ=255)                                              tGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGcaacctaaaatattggtatctccaatattttaggccacacatcaacat                                                                                             <  2:391434‑M1/141‑49 (MQ=255)                                               gCGATTGAGACCGTTATATATATTAGTAGGAGGGTAATATATATTTAACGCACGATATGTGACTATTAGCCTTCGACTCTGTTATGTTGATGTTTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGcatcaacatc                                                                                            <  2:138443/141‑1 (MQ=255)                                                        aaCGGTATATATATTAATAGGAGGGTAAGATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCt                                                                                   <  2:223033/141‑1 (MQ=255)                                                                         tAGGAGTGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTTGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAAcaca                                                                  <  2:25882/141‑1 (MQ=255)                                                                            gaggGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCg                                                               <  1:77535/141‑1 (MQ=255)                                                                             aggGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAATACAGCgg                                                              >  2:310789/1‑140 (MQ=255)                                                                             aggGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACCGCgt                                                              >  1:2837/1‑141 (MQ=255)                                                                              gggTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCgtg                                                             >  2:292671/1‑141 (MQ=255)                                                                                    tatatatTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTAttt                                                       >  1:373845/1‑141 (MQ=255)                                                                                      tatatTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCa                                                     >  1:356003/1‑141 (MQ=255)                                                                                       atatTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGGATGTTATTTCAt                                                    >  2:301850/1‑141 (MQ=255)                                                                                              aCGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCg                                             >  2:82529/1‑141 (MQ=255)                                                                                                gCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCgtg                                           <  2:140466/141‑1 (MQ=255)                                                                                                 cACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCgtgt                                          >  1:66761/1‑141 (MQ=255)                                                                                                  acaatatTGGACTATTAGCTTTCGACTTTGTTATGTTGATGGGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATGAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTa                                         <  2:88276/138‑1 (MQ=255)                                                                                                  aCGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTa                                         >  1:185804/1‑141 (MQ=255)                                                                                                   cGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTAc                                        >  2:175804/1‑141 (MQ=255)                                                                                                   cGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTAATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTACGTGTAc                                        >  2:355578/1‑141 (MQ=255)                                                                                                         gggACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATAAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTc                                  >  1:173505/1‑141 (MQ=255)                                                                                                               aTTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTGACTTCATTAAAACACAGCGTGTTCTTCTATGCGTCCGTGTACAGTTTCAATAtt                            <  1:297171/141‑1 (MQ=255)                                                                                                                ttAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATAttt                           <  1:61216/141‑1 (MQ=255)                                                                                                                ttAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATAttt                           <  1:288567/141‑1 (MQ=255)                                                                                                                       tCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTAAATATTTGATTtca                    >  1:9261/1‑141 (MQ=255)                                                                                                                        cGACTTTGTTATGGTGATGTGGGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTtcat                   <  2:190584/141‑1 (MQ=255)                                                                                                                         gACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTtcatc                  >  1:106520/1‑141 (MQ=255)                                                                                                                          aCTTTGTTATGTTTATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAATCACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTtcatca                 <  2:181026/141‑1 (MQ=255)                                                                                                                               gTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTTCATCATTTTg            >  1:60979/1‑141 (MQ=255)                                                                                                                                  aTGTTGATGcaacctaaaatattggtatctccaatattttaggccacacatcaacataacaaagtcgaaggctaatagtcccatatcgtgcgttaaatatatattaccctcctattaatatatataccgttcccgatagaa         >  2:310260‑M1/1‑9 (MQ=255)                                                                                                                                  aTGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGcatcaacataacaaagtcgaaggctaatagtcccatatcgtgcgttaaatatatattaccctcctattaatatatataccgttcccgatcgca         <  2:391434‑M2/141‑94 (MQ=255)                                                                                                                                   tGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTTCATCATTTTgtagt        <  2:373845/141‑1 (MQ=255)                                                                                                                                    gTTGATGcaacctaaaatattggtatctccaatattttaggccacacatcaacataacaaagtcgaaggctaatagtcccatatcgtgcgttaaatatatattaccctcctattaatatatataccgttcccgatcgcacg       <  2:305529‑M1/141‑135 (MQ=255)                                                                                                                                    gTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGcatcaacataacaaagtcgaaggctaatagtcccatatcgtgcgttaaatatatattaccctcctattaatatatataccgttcccgatcgcacg       <  1:29207‑M2/141‑96 (MQ=255)                                                                                                                                     ttGATGcaacctaaaatattggtatctccaatattttaggccacacatcaacataacaaagtcgaaggctaatagtcccatatcgtgcgttaaatatatattaccctcctattaatatatataccgttcccgatcgcacga      <  2:397555‑M1/141‑136 (MQ=255)                                                                                                                                      tGATGcaacctaaaatattggtatctccaatattttaggccacacatcaacataacaaagtcgaaggctaatagtcccatatcgtgcgttaaatatatattaccctcctattaatatatataccgttcccgatcgcacgat     <  2:393864‑M1/141‑137 (MQ=255)                                                                                                                                       gATGcaacctaaaatattggtatctccaatatattaggccacacatcaacataacaaagtcgaaggctaatagacccatatcgtgcgttaaatatatattaccctcctattaatatatataccgttcccgatcgcacgata    >  2:379197‑M1/1‑4 (MQ=255)                                                                                                                                        aTGTGTGGCCTAAAATGTTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTTCATCATTTTGTAGTAagag   <  1:264738/141‑1 (MQ=255)                                                                                                                                         tgtgtgGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTGCCGTGTACAGTTTCAATATGTGATTTCATCATTTTGTAGTAAGAGt  >  1:188623/1‑141 (MQ=255)                                                                                                                                         tgtgtgGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGAGTACTAAAGAATGTTTGCAAATACAGTTTCAATATTTGATTTCAAAATTTTATAGTAagatt  >  2:394483/1‑139 (MQ=255)                                                                                                                                          |                                                                                                                                            GCTTTTCTCTTTCGTTCAAAGAGAAGTTCTAATACCACCATATCGTGCGATCGGGAACGGTATATATATTAATAGGAGGGTAATATATATTTAACGCACGATATGGGACTATTAGCCTTCGACTTTGTTATGTTGATGTGTGGCCTAAAATATTGGAGATACCAATATTTTAGGTTGCATCAACATCAATTCATCTTACTTCATTAAAACACAGCGTGTTATTTCATGCTTCCGTGTACAGTTTCAATATTTGATTTCATCATTTTGTAGTAAGAGT  >  USA300TCH1516_ALE/705192‑705468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.