New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2278438 =	42 (0.910)	3 (0.070)	3/238	NT	6.9%	intergenic (+106/+213)	mtlD/ebh_3	Mannitol‑1‑phosphate 5‑dehydrogenase/Extracellular matrix‑binding protein ebh
	?	USA300TCH1516_ALE	2278497 =	43 (1.020)					intergenic (+165/+154)	mtlD/ebh_3	Mannitol‑1‑phosphate 5‑dehydrogenase/Extracellular matrix‑binding protein ebh

ATGAAATAATTGAAGCGTACAATTCACTTTCATAATTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAAC  >  USA300TCH1516_ALE/2278298‑2278578                                                                                                                                             |                                                                                                                                             tgtgaacatctagttatttcatagggaaatattccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgca                                                                                                                                              >  2:201490‑M1/141‑141 (MQ=255)   tgaacatctagttatttcatagggaaatattccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcaaa                                                                                                                                            >  1:60949‑M1/139‑141 (MQ=255)     aacatctagttatttcatagggaaatattccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcaaaaa                                                                                                                                          <  1:113222‑M1/5‑1 (MQ=255)     aacatctagttatttcatagggaaatattccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcaaaaa                                                                                                                                          >  2:75701‑M1/137‑141 (MQ=255)     aacatctagttatttcatagggaaatattccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcaaaaa                                                                                                                                          <  1:262401‑M1/5‑1 (MQ=255)      acatctagttatttcatagggaaatattccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcAAAAAt                                                                                                                                         >  1:425036‑M1/136‑141 (MQ=255)        atctagttatttcatagggaaatattccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcAAAAATAc                                                                                                                                       >  1:569265‑M1/134‑141 (MQ=255)            gAAGCGTACAATTCACTTTCATAATTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTccc                                                                                                                                   <  1:698651/141‑1 (MQ=255)              aGCGTACAATTCACTTTCATAATTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCtt                                                                                                                                 >  2:118425/1‑141 (MQ=255)                        tCACTTTCATAATTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGac                                                                                                                       <  1:336932/141‑1 (MQ=255)                          aCTTTCATAATTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGacac                                                                                                                     <  1:225793/141‑1 (MQ=255)                          aCTTTCATAATTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGacac                                                                                                                     <  1:621948/141‑1 (MQ=255)                                ttccttactaagtaaccaagtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcAAAAATACTCCCTTCAACATAGACACTTAACt                                                                                                               >  1:521641‑M1/110‑141 (MQ=255)                                   aTTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTtgt                                                                                                            >  2:53494/1‑141 (MQ=255)                                     ttATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTgtgt                                                                                                          >  1:768845/1‑141 (MQ=255)                                       aTTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTATCTTGTGTta                                                                                                        <  1:691486/141‑1 (MQ=255)                                               ttgtttgAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGaa                                                                                                >  2:43440/1‑141 (MQ=255)                                                  agtctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAgg                                                                                             >  1:491100‑M1/92‑141 (MQ=255)                                                    tgAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAg                                                                                           <  2:127664/141‑1 (MQ=255)                                                    tctaacagttaatatgaatttgttttagtaatgaccaatagccattgaataggtggctgtggctcgaaaataaaacaaattattaacgcAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAg                                                                                           >  2:200384‑M1/90‑141 (MQ=255)                                                           agaagTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTAttttt                                                                                    >  1:516823/1‑141 (MQ=255)                                                             aagTTTCCAACGTTATNCGTTAACAATCANTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGc                                                                                  >  1:740637/1‑141 (MQ=255)                                                                tttCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGtt                                                                               >  1:340843/1‑141 (MQ=255)                                                                tttCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGtt                                                                               >  1:441678/1‑141 (MQ=255)                                                                     aaCGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGTATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTtaataa                                                                          <  1:39747/141‑1 (MQ=255)                                                                       cGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAAtt                                                                        <  1:121742/141‑1 (MQ=255)                                                                            ttCGTTAACAATCAGTAATAATTTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGttt                                                                   <  2:278188/141‑1 (MQ=255)                                                                            ttCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGttt                                                                   >  1:252198/1‑141 (MQ=255)                                                                            ttCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGttt                                                                   >  2:284820/1‑141 (MQ=255)                                                                              cGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTa                                                                 <  1:764756/141‑1 (MQ=255)                                                                              cGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTa                                                                 >  1:112239/1‑141 (MQ=255)                                                                                     aaTCCGTAATAATGTAGTAGTTCCCTTGAATTAACAATACTAAATTTCTGAACATAAACAATCCCCCCTTCCACATAGTCTCTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGa                                                          <  1:157350/141‑1 (MQ=255)                                                                                       tCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagc                                                        <  1:528852/141‑1 (MQ=255)                                                                                       tCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagc                                                        <  2:152099/141‑1 (MQ=255)                                                                                              taatGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagccacagcc                                                 >  1:347578/1‑141 (MQ=255)                                                                                                atGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagccacagccac                                               >  2:24115/1‑141 (MQ=255)                                                                                                atGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGagccacagccac                                               <  2:153167/141‑1 (MQ=255)                                                                                                 tGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCAcc                                              <  2:315018/141‑1 (MQ=255)                                                                                                 tGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCAcc                                              <  2:235955/141‑1 (MQ=255)                                                                                                  gtagtaGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCt                                             >  1:405311/1‑141 (MQ=255)                                                                                                      tagtGCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTc                                         <  1:627453/141‑1 (MQ=255)                                                                                                          tCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGATAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCacaa                                     >  2:63412/1‑138 (MQ=255)                                                                                                               tGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGCCACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTAt                                <  2:155346/141‑1 (MQ=255)                                                                                                               tGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTAt                                <  1:553241/141‑1 (MQ=255)                                                                                                                      aCAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCAt                         >  1:53402/1‑141 (MQ=255)                                                                                                                      aCAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCAt                         >  2:50323/1‑141 (MQ=255)                                                                                                                         atatTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTAc                      <  1:305970/141‑1 (MQ=255)                                                                                                                               aaTTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAAc                >  1:350519/1‑141 (MQ=255)                                                                                                                                     tGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTc          >  1:145621/1‑141 (MQ=255)                                                                                                                                     tGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCAACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTc          >  1:583326/1‑141 (MQ=255)                                                                                                                                      gAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCa         >  1:615125/1‑141 (MQ=255)                                                                                                                                       aaCATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCat        >  1:36010/1‑141 (MQ=255)                                                                                                                                        aCATAAAAAATACTCCCTTCAACCTAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTACTTTCGAGCCACAGCCACCTATTCACTGGCTATTGGTCATTACTAAAACAAATTCata       >  1:579548/1‑141 (MQ=255)                                                                                                                                         cATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCatat      >  1:168463/1‑141 (MQ=255)                                                                                                                                            aaaaaaTACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGGATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTaa   >  2:109737/1‑141 (MQ=255)                                                                                                                                             AAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAAc  >  1:524149‑M1/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             ATGAAATAATTGAAGCGTACAATTCACTTTCATAATTTATTGAGCTTTGTTTGAAACAAGAAGTTTCCAACGTTATTCGTTAACAATCAGTAATAATGTAGTAGTTCCCTTGAATTAACAATATTAAATTTCTGAACATAAAAAATACTCCCTTCAACATAGACACTTAACTTGTGTTATGTATGAAAGGAGTATTTTTGCGTTAATAATTTGTTTTATTTTCGAGCCACAGCCACCTATTCAATGGCTATTGGTCATTACTAAAACAAATTCATATTAAC  >  USA300TCH1516_ALE/2278298‑2278578

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.