New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1378545	59 (0.900)	4 (0.060)	4/248	NT	7.5%	coding (6/1647 nt)	opuD_1	Glycine betaine transporter OpuD
	?	USA300TCH1516_ALE	= 1378579	42 (0.670)					coding (40/1647 nt)	opuD_1	Glycine betaine transporter OpuD

ATCCTATAAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGAAAAGTTAGGTTGGTATTATCT  >  USA300TCH1516_ALE/1378442‑1378715                                                                                                                                          |                                                                                                                                         aTCCTAGAAAGGTGCGTGCTGTATTTAATAAAATGTTTATGTAATTATTATATTCTACTACATAAGATTAAATATAGAAGTTAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTat                                                                                                                                        >  2:89787‑M2/1‑138 (MQ=255)   ccTATAAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAACAGGAAATATAGAATTGAAGGGAGTAATTAATTATGCATTCTGCTTCACGACAAAATCCAACTGACAAGACGTagtg                                                                                                                                      <  2:582634‑M2/140‑5 (MQ=255)   ccTATAAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGCAGTattc                                                                                                                                      <  1:743314‑M2/140‑5 (MQ=255)      ataAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCAcc                                                                                                                                   <  1:154900/140‑1 (MQ=255)       taAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCGACTACATAAAATTAAATATAAAATTGAAGGGAGTAATTAATTATGAATTCTTATTCAGCAGAGAATCCAAATGGAAAGAAGTACTCAccc                                                                                                                                  >  2:404521/1‑139 (MQ=255)        aaaGGTGTGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAg                                                                                                                                 <  2:638288/140‑1 (MQ=255)        aaaGGTGCGTTAGTTATTTAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAAGTATGAATTCTTCTACTACTAATATTGTTGATGGAAAGAAGTATTCACCAg                                                                                                                                 <  1:764259/140‑1 (MQ=255)        aaaGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCTCCAGAGAATCCAAATGGAAAGAAGTATTCACCAg                                                                                                                                 <  1:344002/140‑1 (MQ=255)        aaaGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCCGAGAATCCAAATGGAAAGAAGTATTCACCAg                                                                                                                                 <  1:657289/140‑1 (MQ=255)                gTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATc                                                                                                                         >  1:395316/1‑140 (MQ=255)                   gtgtATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCtat                                                                                                                      <  2:394846/137‑1 (MQ=255)                    gTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCtata                                                                                                                     <  1:602310/140‑1 (MQ=255)                        ttGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGc                                                                                                                 >  2:393318/1‑140 (MQ=255)                            aTAAAATGTTTAGATAATATTTTGATTCTACTACATAAAATTAAAGAGAGAATTGAAGGGAGTAATTAATTATTAATTCTTCTGCACCAGAGAATCCGAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAAtt                                                                                                             <  1:563952/140‑1 (MQ=255)                                         ataataTTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAg                                                                                                >  2:580571/1‑140 (MQ=255)                                            atatatatATTCTACTACATAAAATTAAATATACAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCg                                                                                             <  1:161197/140‑1 (MQ=255)                                            atatTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCg                                                                                             <  1:164588/140‑1 (MQ=255)                                            atatTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCg                                                                                             <  2:220836/140‑1 (MQ=255)                                             tgtttttATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGt                                                                                            >  2:140099/3‑140 (MQ=255)                                             tatTTTTATTGATATATATAAAGTTAAATATAGAATTGAAGGGAGTAATTAATTATGCATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTAACCAGTCTTCATCTATAGTGCAATTGTTGTTACTATAGTCGt                                                                                            >  2:492731/1‑140 (MQ=255)                                             tatTTTTATTCTACTACATACAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATGCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTACAATTGTTGTTGCTATAGTCGt                                                                                            >  2:475310/1‑140 (MQ=255)                                                          ctacATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCa                                                                               <  2:51836/140‑1 (MQ=255)                                                           tacATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGAAt                                                                              >  2:313597/1‑140 (MQ=255)                                                             cATAATATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCAttt                                                                            <  1:22452/140‑1 (MQ=255)                                                             cATAAAATTAAACATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAAGCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCAttt                                                                            <  1:717644/140‑1 (MQ=255)                                                                 aaaTTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTattcataattaattactcccttcaattctatatttaattt                                                                                                  >  2:739953‑M2/1‑74 (MQ=255)                                                                 aaaTTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTattcataattaattactcccttcaattctatatttaattt                                                                                                  <  1:739953‑M2/114‑41 (MQ=255)                                                                    ttAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCCGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTg                                                                     >  2:227687/1‑140 (MQ=255)                                                                     tAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTattcataattaattactcccttcaattctatattta                                                                                                      >  2:656899‑M2/1‑70 (MQ=255)                                                                     tAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTattcataattaattactcccttcaattctatattta                                                                                                      <  1:656899‑M2/106‑37 (MQ=255)                                                                     tAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGa                                                                    <  2:651098/140‑1 (MQ=255)                                                                      aaaTATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTATGTTGTGCATTTTTACCTGaa                                                                   <  1:154721/140‑1 (MQ=255)                                                                      aaaTATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTGCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGaa                                                                   <  2:181192/140‑1 (MQ=255)                                                                       tatacAGAGTTGAATGGAGTAATTCAGTGTGATTTCTTCTTCACCAGAGGATCCAAATGGAAAGAAGTATTCACCAGTTTTCATCTATAGTGCTATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAAc                                                                  <  2:317395/139‑1 (MQ=255)                                                                       aaTATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAAc                                                                  <  2:291791/140‑1 (MQ=255)                                                                       aaTATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAAc                                                                  <  1:438910/140‑1 (MQ=255)                                                                       aaTAGATAATTGAAGGGAGGAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAAc                                                                  <  2:103055/140‑1 (MQ=255)                                                                             gAATTGAAGGGAGCAATTAATTACGGGTGCTACGTCACCAGAGAATCCAAATGGAAAGAAGTATTCATCAGGCTACATCTATAGTGCAATTTTGGTTGCTATATTCGTATTACTTGGTGCATTTTTACTTGCACAAGTCa                                                            >  2:398689/1‑140 (MQ=255)                                                                                     gggAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCAGAACAATTCAACTATGtt                                                    <  2:98899/140‑1 (MQ=255)                                                                                        aGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCt                                                                      >  2:436669/1‑119 (MQ=255)                                                                                        aGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCt                                                                      <  2:470087/119‑1 (MQ=255)                                                                                        aGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCt                                                                      <  1:436669/119‑1 (MQ=255)                                                                                        aGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCt                                                                      >  1:470087/1‑119 (MQ=255)                                                                                        aGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACCTGGTGCATTTTTACCt                                                                      >  2:45040/1‑119 (MQ=255)                                                                                        aGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACCTGGTGCATTTTTACCt                                                                      <  1:45040/119‑1 (MQ=255)                                                                                            attaattaTGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCCACTATGTTACCaata                                             >  1:638739/1‑140 (MQ=255)                                                                                            attaattaTGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCaata                                             >  1:639559/1‑140 (MQ=255)                                                                                                  taTGCATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTa                                       <  1:215255/140‑1 (MQ=255)                                                                                                     gAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTaaaa                                    <  1:393318/140‑1 (MQ=255)                                                                                                          cttcttcACCAGAGAATCCAAATGGACAGCAGTATTCACCAGACTTCATCTATAGTGCAATTGTTGTTGCTATAGACGTATTACTTTGTTCATTTTTACCCGAACAATGCAACTATGTTACCAATAATATTAATATATgg                               >  2:552569/1‑140 (MQ=255)                                                                                                                    agagAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGaaa                     >  2:383481/1‑140 (MQ=255)                                                                                                                       gaATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGAAAAGt                  <  2:429893/140‑1 (MQ=255)                                                                                                                         aTCCGAAGGGAAAGAAGTAGTCACCAGTCTTCATCTATAGTGGAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGAAAAGTTa                <  2:743314/140‑1 (MQ=255)                                                                                                                         aTCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGACTTACATAAAAGTTa                >  2:769281/1‑140 (MQ=255)                                                                                                                                    aataagTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGAAAAGTTAGGTTGGtatta     <  2:31088/137‑1 (MQ=255)                                                                                                                                    aagaagTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGAAAAGTTAGGTTGGtatta     <  2:340805/140‑1 (MQ=255)                                                                                                                                       aagTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGAAAAGTTAGGTTGGTATTATCt  <  2:693932/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                         ATCCTATAAAGGTGCGTGAGTTATTGAATAAAATGTTTAGATAATATTTTTATTCTACTACATAAAATTAAATATAGAATTGAAGGGAGTAATTAATTATGAATTCTTCTTCACCAGAGAATCCAAATGGAAAGAAGTATTCACCAGTCTTCATCTATAGTGCAATTGTTGTTGCTATAGTCGTATTACTTGGTGCATTTTTACCTGAACAATTCAACTATGTTACCAATAATATTAAAATGTGGATTACAGAAAAGTTAGGTTGGTATTATCT  >  USA300TCH1516_ALE/1378442‑1378715

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.