New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1336678	48 (0.740)	3 (0.050)	3/240	NT	6.2%	coding (341/369 nt)	glnR	glutamate‑‑ammonia ligase repressor
	?	CP000730	= 1336691	46 (0.760)					coding (354/369 nt)	glnR	glutamate‑‑ammonia ligase repressor

AAAAGGATTTAATATCAAAGGGATTAAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTT  >  CP000730/1336538‑1336816                                                                                                                                             |                                                                                                                                           aaaaGGATTTAATATCAAAGGGATTAAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCG                                                                                                                                            >  2:646611‑M1/1‑141 (MQ=255)  aaaGGATTTAATATCAAAGGGATTAAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCgt                                                                                                                                           >  2:311132/1‑141 (MQ=255)         ttAATATCAAAGGGATTAAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGAtt                                                                                                                                    >  2:258144/1‑141 (MQ=255)         ttAATATCAAAGGGATTAAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAAAAAAAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGAtt                                                                                                                                    <  2:435377/141‑1 (MQ=255)                   aGGGATTAAACAAATCATTTATGACTCACAAAAGCAATTAACAACAGAAGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGggataaatcaccacgatt                                                                                                                          <  2:425867‑M1/141‑19 (MQ=255)                          aaaCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaa                                                                                                                   <  1:521862/141‑1 (MQ=255)                          aaaCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaa                                                                                                                   <  2:495406/141‑1 (MQ=255)                          aaaCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaa                                                                                                                   >  1:369877/1‑141 (MQ=255)                           aaCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaat                                                                                                                  >  2:97166/1‑141 (MQ=255)                           aaCAAATCATTTATGACTCACAAGAGAATTTAACGACAGGTGAACAAGAGATAAGAAAAAAGAGGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaat                                                                                                                  <  1:350770/141‑1 (MQ=255)                            aCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaata                                                                                                                 <  1:650614/141‑1 (MQ=255)                                 taaTTTATGACTCACAAAAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAAtt                                                                                                            <  1:363260/139‑1 (MQ=255)                                    tttATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTgg                                                                                                         >  1:225734/1‑141 (MQ=255)                                    tttATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTgg                                                                                                         >  1:225824/1‑141 (MQ=255)                                       aTGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTGATTAAATAAAATTTggagg                                                                                                      >  1:205946/1‑141 (MQ=255)                                        tGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTggagga                                                                                                     >  1:767062/1‑141 (MQ=255)                                          aCTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGAtt                                                                                                   <  1:227022/141‑1 (MQ=255)                                           cTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGAttt                                                                                                  <  1:331867/141‑1 (MQ=255)                                            tCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCACGATTTATTAAATAAAATTTGGAGGAtttt                                                                                                 >  2:208925/1‑141 (MQ=255)                                                       tttAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCaaa                                                                                      <  1:189137/141‑1 (MQ=255)                                                        ttAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCaaaa                                                                                     >  2:211773/1‑141 (MQ=255)                                                              acaGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACt                                                                               <  1:753024/141‑1 (MQ=255)                                                                aGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACttt                                                                             >  2:278615/1‑141 (MQ=255)                                                                        aaGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATATGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAg                                                                     >  2:54031/1‑141 (MQ=255)                                                                                   aaaaaGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGt                                                          >  1:114711/1‑141 (MQ=255)                                                                                   aaaaaGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGt                                                          >  2:347314/1‑141 (MQ=255)                                                                                   aaaaaGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGt                                                          >  2:323533/1‑141 (MQ=255)                                                                                        gatgatTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGggataaatcaccacgatttattg                                                                                                                     <  1:609985‑M1/77‑24 (MQ=255)                                                                                        gatgatTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGggataaatcaccacgatttattg                                                                                                                     >  2:609985‑M1/1‑54 (MQ=255)                                                                                        gatgagTGTAGATGCCACGCAAAAGCCTAGTGGTGAAACTTTGCCAGTAGATCGTACGTATTTAGCCCATATTATTAAATAAGATGTGGAGGATTTTAAAATGCCAAAACGTACTGTCACTAAAGACGACATTCGTAAAtt                                                     <  1:781873/141‑1 (MQ=255)                                                                                              tGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCaga                                               <  2:767062/141‑1 (MQ=255)                                                                                                   aTGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAgg                                          <  1:311132/141‑1 (MQ=255)                                                                                                       cACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGaaaa                                      <  2:670996/141‑1 (MQ=255)                                                                                                                gCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGata                             <  2:110380/141‑1 (MQ=255)                                                                                                                gCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGata                             >  1:561068/1‑141 (MQ=255)                                                                                                                 ccTATTGGAAAAACTTTGCCAATAAATCGTGGTGATTTAACACGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGatat                            <  2:400480/141‑1 (MQ=255)                                                                                                                     ttGGAGAAACTTTGCCAATAAATAGTGGTGATTTATACCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTaa                        >  2:465804/1‑141 (MQ=255)                                                                                                                        gagaAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGAt                     <  1:420864/141‑1 (MQ=255)                                                                                                                         agaAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGAtt                    <  2:88375/141‑1 (MQ=255)                                                                                                                         agaAACGTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAAGGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGAtt                    <  2:543856/141‑1 (MQ=255)                                                                                                                          gaAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTa                   >  2:779991/1‑141 (MQ=255)                                                                                                                             aCTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACaa                >  2:522560/1‑141 (MQ=255)                                                                                                                                 tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTCAGATTACAATTCa            >  2:79506/1‑141 (MQ=255)                                                                                                                                 tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCa            >  1:511956/1‑141 (MQ=255)                                                                                                                                 tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCa            >  2:768158/1‑141 (MQ=255)                                                                                                                                 tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCa            >  2:141700/1‑141 (MQ=255)                                                                                                                                 tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCa            >  1:730977/1‑141 (MQ=255)                                                                                                                                  gCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCATAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCAc           >  2:492049/1‑141 (MQ=255)                                                                                                                                  gCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCAc           >  2:726399/1‑141 (MQ=255)                                                                                                                                   ccAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACt          <  1:67386/141‑1 (MQ=255)                                                                                                                                   ccAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACt          <  1:198346/141‑1 (MQ=255)                                                                                                                                    cAATAAATCGTGGTGATTTATCCcgatttattggcaaagtttctccaataggcttttgcgtggcatctacaatcatc                                                                         <  1:609985‑M2/77‑55 (MQ=255)                                                                                                                                    cAATAAATCGTGGTGATTTATCCcgatttattggcaaagtttctccaataggcttttgcgtggcatctacaatcatc                                                                         >  2:609985‑M2/1‑23 (MQ=255)                                                                                                                                     aaTAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGa        <  1:592819/141‑1 (MQ=255)                                                                                                                                        aaaTCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGatat     >  1:763460/1‑141 (MQ=255)                                                                                                                                         aaTCGTGGTGATTTATCCcgatttattggcaaagtttctccaataggcttttgcgtggcatctacaatcatcttttttcttatctcttgttcttctgttgttaattgcttttgtgagtcataaatgatttgtttaatccct    <  2:425867‑M2/141‑124 (MQ=255)                                                                                                                                         aaTCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATAtt    >  2:188700/1‑141 (MQ=255)                                                                                                                                           tCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATAtttt  <  2:540811/141‑1 (MQ=255)                                                                                                                                           tCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATAtttt  <  1:531059/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                           AAAAGGATTTAATATCAAAGGGATTAAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTT  >  CP000730/1336538‑1336816

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