New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103358 =	122 (0.520)	49 (0.210)	13/196	23.4	0.38	intergenic (‑358/+60)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	1253897 =	41 (0.170)					intergenic (+55/+36)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

CGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCGGG  >  NC_014034/1253835‑1253996                                                                        |                                                                                                    cGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGaa                                                                        >  1:3231929/1‑101 (MQ=12)  gAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGaaa                                                                       >  1:4508645/1‑101 (MQ=12)   aaaTAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAAt                                                                      >  1:4267535/1‑101 (MQ=9)     aTAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATcc                                                                    >  2:639659/1‑101 (MQ=9)      tAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGaaaccat                                                                   >  2:594676/1‑97 (MQ=9)      tAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGCGTCGCCTCGGCGAAAGCCGAGGCGAAATCct                                                                   >  1:3388999/1‑101 (MQ=9)       aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGGGAAATCctc                                                                  >  1:2488799/1‑101 (MQ=9)       aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                                                                  >  2:3217084/1‑101 (MQ=9)       aaaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctc                                                                  >  2:3461878/1‑101 (MQ=9)        aaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctct                                                                 >  1:560763/1‑101 (MQ=9)        aaCCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGCGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCctcc                                                                 >  2:3834626/1‑100 (MQ=9)          ccGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCa                                                               >  2:232299/1‑101 (MQ=9)           cGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCAc                                                              >  2:3932591/1‑101 (MQ=9)            gATCCCGGCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                                                             >  2:3495038/1‑101 (MQ=2)            gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                                                             >  1:3314571/1‑101 (MQ=9)            gATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACg                                                             >  1:1324093/1‑101 (MQ=9)             aTCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACgg                                                            >  1:267112/1‑101 (MQ=9)               cccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCt                                                          >  1:3837810/1‑101 (MQ=9)               cccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCt                                                          >  2:1738854/1‑101 (MQ=9)                ccgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCtt                                                         >  2:2470840/1‑101 (MQ=9)                 cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTc                                                        >  2:4459402/1‑101 (MQ=9)                 cgccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTc                                                        >  1:1596956/1‑101 (MQ=9)                  gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGTAAGCCGAGGCGAAATCCTCTCACGGCTTcc                                                       >  1:317126/1‑101 (MQ=9)                  gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTcc                                                       >  2:12113/1‑101 (MQ=9)                  gccccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTcc                                                       >  1:3967434/1‑101 (MQ=9)                    cccgcTCTCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAg                                                     >  1:2801068/1‑101 (MQ=9)                        ctctCATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCa                                                 >  2:298667/1‑101 (MQ=9)                         tctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAg                                                >  2:4600741/1‑101 (MQ=9)                         tctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAg                                                >  1:645515/1‑101 (MQ=9)                         tctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAg                                                >  1:851690/1‑101 (MQ=9)                         tctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAg                                                >  1:2344959/1‑101 (MQ=9)                          ctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAgg                                               >  1:1857792/1‑101 (MQ=9)                          ctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAgg                                               >  1:745954/1‑101 (MQ=9)                          ctcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCCCGGCGAAAGCCGAGGCGGAATCCTCTCACCGGTTTCCGTTCAgg                                               >  1:911833/1‑101 (MQ=0)                           tcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGa                                              >  1:4748710/1‑101 (MQ=9)                           tcATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTACAGTTCAGGa                                              >  2:532986/1‑101 (MQ=9)                            cATCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaa                                             >  1:3867763/1‑101 (MQ=9)                             aTCTTGCCCTAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCTCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGaaa                                            >  1:1500962/1‑101 (MQ=9)                                                            gcggagcccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCg             >  1:3477216/11‑101 (MQ=255)                                                              ggagcccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAt           >  2:1741299/9‑101 (MQ=255)                                                              ggagcccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAt           >  1:275521/9‑101 (MQ=255)                                                              ggagcccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAt           >  2:3252578/9‑101 (MQ=255)                                                              ggagcccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAt           >  2:2513085/9‑101 (MQ=255)                                                              gccccccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAt           <  2:1793456/93‑1 (MQ=255)                                                               gcccccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAtt          <  2:1166108/94‑1 (MQ=255)                                                               gcccccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAtt          <  1:672098/94‑1 (MQ=255)                                                               agcccccgcccGGGTCGCCTCGGCAAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAtt          <  2:2800903/92‑1 (MQ=38)                                                                agcccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAttt         >  2:707858/7‑101 (MQ=255)                                                                agcccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAttt         <  1:2443802/95‑1 (MQ=255)                                                                   ccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCCGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTtctc      >  2:2670330/4‑101 (MQ=255)                                                                   ccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTtctc      >  2:334759/4‑101 (MQ=255)                                                                   ccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTtctc      <  1:3684288/98‑1 (MQ=255)                                                                   ccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTtctc      >  2:644487/4‑101 (MQ=255)                                                                   ccccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTtctc      >  2:292893/4‑101 (MQ=255)                                                                   cccagcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTtctc      <  1:1477530/97‑1 (MQ=255)                                                                    ccgcccGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTcc     <  1:4609390/97‑1 (MQ=255)                                                                    cccgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTcc     >  1:2804533/3‑101 (MQ=255)                                                                     cgcccGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCg    <  1:1661155/98‑1 (MQ=255)                                                                      cgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCgg   <  2:3910912/101‑1 (MQ=255)                                                                      cgcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCgg   >  2:121734/1‑101 (MQ=255)                                                                      ccccGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCgg   <  2:1760927/99‑1 (MQ=255)                                                                       gcCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCggg  <  2:2304371/101‑1 (MQ=255)                                                                        |                                                                                                    CGAAATAAACCGATCCCGCCCCGCTCTCATCTTGCCCTAAATACCTCGGGGGTGCG.....GGAG....CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCGGG  >  NC_014034/1253835‑1253996 Base quality scores:  ATCG  < 3 ≤  ATCG  < 19 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG