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

AAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTTAGGAACAATTAAAAA  >  CP000730/1336563‑1336831                                                                                                                                 |                                                                                                                                             aaaCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaa                                                                                                                                  <  1:521862/141‑1 (MQ=255) aaaCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaa                                                                                                                                  >  1:369877/1‑141 (MQ=255) aaaCAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATtaaa                                                                                                                                  <  2:495406/141‑1 (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                                                                         >  2:323533/1‑141 (MQ=255)                                                          aaaaaGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGt                                                                         >  2:347314/1‑141 (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                           >  2:141700/1‑141 (MQ=255)                                                                                                        tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCa                           >  1:511956/1‑141 (MQ=255)                                                                                                        tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCa                           >  1:730977/1‑141 (MQ=255)                                                                                                        tGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCa                           >  2:768158/1‑141 (MQ=255)                                                                                                         gCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCATAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCAc                          >  2:492049/1‑141 (MQ=255)                                                                                                         gCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCAc                          >  2:726399/1‑141 (MQ=255)                                                                                                          ccAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACt                         <  1:198346/141‑1 (MQ=255)                                                                                                          ccAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACt                         <  1:67386/141‑1 (MQ=255)                                                                                                           cAATAAATCGTGGTGATTTATCCcgatttattggcaaagtttctccaataggcttttgcgtggcatctacaatcatc                                                                                        >  2:609985‑M2/1‑23 (MQ=255)                                                                                                           cAATAAATCGTGGTGATTTATCCcgatttattggcaaagtttctccaataggcttttgcgtggcatctacaatcatc                                                                                        <  1:609985‑M2/77‑55 (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                 <  1:531059/141‑1 (MQ=255)                                                                                                                  tCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATAtttt                 <  2:540811/141‑1 (MQ=255)                                                                                                                     tggtgATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTTAgg              >  2:250240/1‑141 (MQ=255)                                                                                                                     tggtgATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTTAgg              <  1:92885/141‑1 (MQ=255)                                                                                                                      ggtgATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATCACAATTCACTGATATTTTAGGa             >  2:717639/1‑141 (MQ=255)                                                                                                                               tCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTTAGGAACAATTaaa    <  2:225824/141‑1 (MQ=255)                                                                                                                               tCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTTAGGAACAATTaaa    <  2:225734/141‑1 (MQ=255)                                                                                                                                 ccGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTTAGGAACAATTaaaaa  <  1:320732/141‑1 (MQ=255)                                                                                                                                 |                                                                                                                                             AAACAAATCATTTATGACTCACAAGAGCATTTAACAACAGATGAACAAGAGATAAGAAAAAAGATGATTGTAGATGCCACGCAAAAGCCTATTGGAGAAACTTTGCCAATAAATCGTGGTGATTTATCCCGATTTATTAAATAAAATTTGGAGGATTTTAAAATGCCAAAACGTACTTTCACTAAAGACGACATTCGTAAATTTGCAGAAGAGGAAAATGTAAGATATTTAAGATTACAATTCACTGATATTTTAGGAACAATTAAAAA  >  CP000730/1336563‑1336831

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.