New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1103358 =	147 (0.610)	52 (0.220)	12/196	21.7	0.36	intergenic (‑358/+60)	ugpB/regA2	sn‑glycerol‑3‑phosphate‑binding periplasmic protein ugpB/photosynthetic apparatus regulatory protein RegA
	?	NC_014034	1253897 =	35 (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                                   >  2:2071688/3‑101 (MQ=32)                                                                    ctAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGAT                                   >  2:1969962/3‑101 (MQ=32)                                                                     tAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATG                                  >  2:4461898/2‑101 (MQ=32)                                                                     tAAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATG                                  >  2:1954379/2‑101 (MQ=32)                                                                      AAATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGA                                 >  2:1334809/1‑101 (MQ=32)                                                                       AATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGAT                                >  2:3727976/1‑101 (MQ=32)                                                                       AATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGAT                                >  1:4125409/1‑101 (MQ=32)                                                                       AATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGAT                                >  1:4018971/1‑101 (MQ=32)                                                                       AATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGAT                                >  2:193610/1‑101 (MQ=32)                                                                       AATACCTCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGAT                                >  2:2446408/1‑101 (MQ=32)                                                                        atacctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATC                               >  1:4146736/7‑101 (MQ=32)                                                                         tacctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCC                              >  2:3025740/6‑101 (MQ=32)                                                                          acctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCG                             >  1:4203828/5‑101 (MQ=32)                                                                          acctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCACTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCG                             >  1:1880712/5‑101 (MQ=17)                                                                           cctCGGGGGTGC.GGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCA                           >  2:4168538/4‑101 (MQ=1)                                                                            ctCGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGAGACGCA                           >  2:2408468/3‑101 (MQ=16)                                                                              CGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGC                         >  1:280850/1‑101 (MQ=32)                                                                              CGGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGC                         >  1:1864881/1‑101 (MQ=32)                                                                               GGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCC                        >  1:385865/1‑101 (MQ=32)                                                                               GGGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCC                        >  1:1693991/1‑101 (MQ=32)                                                                                GGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCC                       >  2:2688040/1‑101 (MQ=32)                                                                                GGGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCC                       >  2:4918021/1‑101 (MQ=32)                                                                                 GGGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCG                      >  2:312837/1‑101 (MQ=32)                                                                                  GGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGG                     >  1:4507298/1‑101 (MQ=32)                                                                                  GGTGCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGG                     >  1:3069058/1‑101 (MQ=32)                                                                                   gtgCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGT                    >  1:2638850/4‑101 (MQ=32)                                                                                    tgCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTG                   >  2:2696591/3‑101 (MQ=31)                                                                                     ggGGGGGCGGCCCCCCCCCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGC                  <  1:3386172/99‑1 (MQ=2)                                                                                     ggGGGGGCGGACCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGC                  <  2:3190353/99‑1 (MQ=1)                                                                                     gCGGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTTCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGC                  >  2:2897215/2‑101 (MQ=11)                                                                                       GGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCCGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  1:83481/1‑101 (MQ=1)                                                                                       GGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  2:1768042/1‑101 (MQ=1)                                                                                       GGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  2:1808640/1‑101 (MQ=1)                                                                                       GGGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                >  2:4519202/1‑101 (MQ=1)                                                                                       GGGGGCGCGCCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGC                <  1:780364/101‑1 (MQ=0)                                                                                        aGGGCGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGCTGATCCGCAGCCCGGTGCGCT               >  1:50977/2‑101 (MQ=1)                                                                                         cgcgccccCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTG              <  1:3585577/93‑1 (MQ=0)                                                                                            CGGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGA           >  2:4934030/1‑101 (MQ=1)                                                                                             gggcCCCGCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          <  2:3701300/97‑1 (MQ=11)                                                                                             ccccCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          <  2:1251963/97‑1 (MQ=1)                                                                                             GGAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGAT          >  1:385677/1‑101 (MQ=1)                                                                                              GAGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATT         >  1:2593273/1‑101 (MQ=1)                                                                                               gcCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        <  1:3634218/99‑1 (MQ=1)                                                                                               ccCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        <  1:4834091/99‑1 (MQ=1)                                                                                               ccCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        <  2:4863526/99‑1 (MQ=1)                                                                                               AGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  2:188010/1‑101 (MQ=1)                                                                                               AGCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  1:1373676/1‑101 (MQ=1)                                                                                               AGCACCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTT        >  2:2105458/1‑101 (MQ=1)                                                                                                GCCCCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTC       >  1:260268/1‑101 (MQ=1)                                                                                                  CCCGGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTC     <  1:62400/101‑1 (MQ=1)                                                                                                   CCCGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCC    <  2:2239745/101‑1 (MQ=1)                                                                                                   CCCCCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCC    <  2:2567642/101‑1 (MQ=1)                                                                                                                                                                                                           GCGGGCGAAGACCTGGGCGGCATGATCGATTTCGAGGACTGATCCCCGGCCCCCGTTTTTTCTTGGCCCAAATACGCCGGGGGTCCGGGGGCGGAGCCCCCG...................................................................................................  <  NC_014034/1103459‑1103358 ....................................................................................................CGCCGGGTCGCCTCGGCGAAAGCCGAGGCGAAATCCTCTCACGGCTTCCAGTTCAGGAAATTCGAGATGATCCGCAGCCCGGTGCGCTGCGATTTCTCCGG  >  NC_014034/1253897‑1253995 Base quality scores:  ATCG  < 3 ≤  ATCG  < 17 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG