New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103358 =	89 (0.400)	37 (0.170)	14/196	25.5	0.38	intergenic (‑358/+60)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	1253897 =	31 (0.140)					intergenic (+55/+36)	RCAP_rcc01181/hisH	hypothetical protein/imidazole glycerol phosphate synthase subunit HisH
Rejected: Position hash score below cutoff.

GCGGGCGAAGACCTGGGCGGCATGATCGATTTCGAGGACTGATCCCCGGCCCCCGTTTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCCG...................................................................................................  <  NC_014034/1103459‑1103358 ....................................................................................................CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCGG  >  NC_014034/1253897‑1253995                                                                                                                                                                                                                                                                              ctAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGAT                                   >  2:4130083/3‑101 (MQ=32)                                                                    ctAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGAT                                   >  1:2612350/3‑101 (MQ=32)                                                                     tAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATG                                  >  1:2891887/2‑101 (MQ=32)                                                                      AAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGA                                 >  1:4261031/1‑101 (MQ=32)                                                                        atacctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATC                               >  2:3921569/7‑101 (MQ=32)                                                                        atacctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATC                               >  1:609870/7‑101 (MQ=32)                                                                        atacctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATC                               >  2:1021168/7‑101 (MQ=32)                                                                         tacctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCC                              >  2:3298075/6‑101 (MQ=32)                                                                         tacctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCC                              >  2:2462834/6‑101 (MQ=32)                                                                          acctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTAAGGAAATTCGAGATGATCCG                             >  1:1476972/5‑101 (MQ=17)                                                                          acctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGGTCAGGAAATTCGAGATGATCCG                             >  2:1734631/5‑101 (MQ=17)                                                                           cctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGC                            >  2:1562085/4‑101 (MQ=33)                                                                              CGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGC                         >  2:133426/1‑101 (MQ=32)                                                                               GGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCC                        >  2:2399808/1‑101 (MQ=32)                                                                               GGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCC                        >  2:1491006/1‑101 (MQ=32)                                                                                GGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCC                       >  1:1151499/1‑101 (MQ=32)                                                                                    tgCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTG                   >  1:1383334/3‑101 (MQ=31)                                                                                       GGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  2:27410/1‑101 (MQ=1)                                                                                        GGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCT               >  1:1987220/1‑101 (MQ=1)                                                                                         ggccccccCCCCCCCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTG              <  1:26638/93‑1 (MQ=0)                                                                                          GGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGC             >  2:3223851/1‑101 (MQ=1)                                                                                            CGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGA           >  2:2647070/1‑101 (MQ=1)                                                                                             ggccCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          <  1:4331141/97‑1 (MQ=1)                                                                                             GGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          >  2:764841/1‑101 (MQ=1)                                                                                             GGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          >  2:1639168/1‑101 (MQ=1)                                                                                              GAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATT         >  1:3383119/1‑101 (MQ=1)                                                                                               gcCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        <  2:1451238/99‑1 (MQ=1)                                                                                               AGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  2:2231343/1‑101 (MQ=1)                                                                                               AGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  2:1863516/1‑101 (MQ=1)                                                                                                GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTC       >  2:3051593/1‑101 (MQ=1)                                                                                                 CCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCc      >  1:3323764/1‑100 (MQ=1)                                                                                                 CCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCT      <  1:1656276/101‑1 (MQ=1)                                                                                                  CCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTC     >  2:2001306/1‑101 (MQ=1)                                                                                                  CCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTC     >  2:1961816/1‑101 (MQ=1)                                                                                                  CCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTC     >  2:1723697/1‑101 (MQ=1)                                                                                                  CCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTC     >  2:3016736/1‑101 (MQ=1)                                                                                                    CCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCG   >  2:1200690/1‑101 (MQ=1)                                                                                                                                                                                                           GCGGGCGAAGACCTGGGCGGCATGATCGATTTCGAGGACTGATCCCCGGCCCCCGTTTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCCG...................................................................................................  <  NC_014034/1103459‑1103358 ....................................................................................................CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCGG  >  NC_014034/1253897‑1253995 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 24 ≤  ATCG  < 32 ≤  ATCG  < 39 ≤  ATCG