New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1396639 =	189 (1.170)	64 (0.400)	7/132	19.6	0.26	coding (521/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	= 1434845	175 (0.710)					intergenic (‑624/‑334)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

TTATCGCCGCATGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC......................................................................................................................................  <  NC_014034/1396683‑1396639 ...............................................................................TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCACCGAGATCACCCTCCTTCAGCGCGTCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC  <  NC_014034/1434845‑1434746                                              ||||||||||||||||||||||||||||||||||                                                                                                     tcgagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCG                                                                                >  2:4872433/9‑101 (MQ=0) tcgagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCG                                                                                >  1:4939798/9‑101 (MQ=0)  cgagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGG                                                                               >  1:1312843/8‑101 (MQ=0)  cgagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGG                                                                               >  1:3858343/8‑101 (MQ=0)  cgagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGG                                                                               >  1:2772735/8‑101 (MQ=0)   gagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGG                                                                              >  2:1431341/7‑101 (MQ=0)   gagccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGG                                                                              >  1:1605103/7‑101 (MQ=0)    agccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                             >  1:4903488/6‑101 (MQ=0)    agccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                             >  2:1590595/6‑101 (MQ=0)    agccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGG                                                                             <  1:3863349/96‑1 (MQ=0)     gccaGCATAGTTTCGATCCACGCCCCCGCGGGGAGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGG                                                                            <  1:4306899/97‑1 (MQ=0)      ccaGCATAGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGG                                                                           <  1:4546155/98‑1 (MQ=0)      ccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGG                                                                           >  2:4551078/4‑101 (MQ=0)      ccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGG                                                                           <  1:879297/98‑1 (MQ=0)      ccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGG                                                                           >  2:4805210/4‑101 (MQ=0)      ccaGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTT.CAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  2:2807018/98‑1 (MQ=0)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGg                                                                          >  2:1410700/3‑100 (MQ=0)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  1:4451178/99‑1 (MQ=1)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  1:4601225/99‑1 (MQ=1)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  1:4665167/99‑1 (MQ=1)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  1:3270682/99‑1 (MQ=1)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          >  1:2438192/3‑101 (MQ=1)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          >  1:216669/3‑101 (MQ=1)       caGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGA                                                                          <  1:1176760/99‑1 (MQ=1)        aGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAG                                                                         >  2:4982795/2‑101 (MQ=1)         GCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                        <  1:4978266/101‑1 (MQ=1)         GCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                        <  2:1663262/101‑1 (MQ=1)         GCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                        <  1:2141749/101‑1 (MQ=1)         GCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                        <  1:910194/101‑1 (MQ=1)         GCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGC                                                                        <  2:2400946/101‑1 (MQ=1)          CATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCG                                                                       <  2:2544048/101‑1 (MQ=1)           ataGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGc                                                                      >  2:1057343/4‑100 (MQ=1)           ataGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                                                                      <  2:310388/98‑1 (MQ=1)           ataGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                                                                      >  1:2871982/4‑101 (MQ=1)           ataGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA                                                                      >  1:2016563/4‑101 (MQ=1)           ataGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGAGTTTCGATCCACGCCCCCGCGGGCGGAGCGA                                                                      >  2:4508980/4‑101 (MQ=0)            taGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC                                                                     >  1:4826273/3‑101 (MQ=1)            taGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCAGGGTGTTTCGATCCACGCCCCCGCGGGGGGGGCGAC                                                                     >  2:4434227/3‑101 (MQ=0)             aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc                                                                    <  1:4161174/100‑2 (MQ=1)             aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc                                                                    >  2:3598721/2‑100 (MQ=1)             aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc                                                                    >  1:3451392/2‑100 (MQ=1)             aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc                                                                    >  1:223518/2‑100 (MQ=1)             aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg                                                                    >  2:664653/2‑100 (MQ=1)              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACca                                                                   >  2:1546071/1‑99 (MQ=1)              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACca                                                                   >  2:2170493/1‑99 (MQ=1)              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACca                                                                   >  2:2790760/1‑99 (MQ=1)              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACca                                                                   >  1:3772024/1‑99 (MQ=1)              GTTTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACca                                                                   >  1:3168975/1‑99 (MQ=1)                TTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcacc                                                                 >  2:4470856/1‑97 (MQ=1)                TTCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCCCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcacc                                                                 <  2:1945034/101‑5 (MQ=1)                 TCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccg                                                                >  1:490431/1‑96 (MQ=1)                 TCGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccg                                                                <  2:618979/101‑6 (MQ=1)                  CGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccgg                                                               >  1:4752711/1‑95 (MQ=1)                  CGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccgg                                                               <  1:4553690/101‑7 (MQ=1)                  CGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccgg                                                               >  1:4446630/1‑95 (MQ=1)                  CGATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccgg                                                               >  1:3778561/1‑95 (MQ=1)                   GATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggc                                                              >  1:1988851/1‑94 (MQ=1)                   GATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggc                                                              >  1:2483963/1‑94 (MQ=1)                   GATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggc                                                              >  1:4574011/1‑94 (MQ=1)                    ATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcc                                                             >  1:28874/1‑93 (MQ=1)                    ATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcc                                                             <  1:4833911/101‑9 (MQ=1)                    ATCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcc                                                             >  1:2028608/1‑93 (MQ=1)                     TCCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcct                                                            <  1:2083580/101‑10 (MQ=0)                      CCACGCCCCCGCGGGGGGAGCGACATCCTGTTCCAGACGCACTCGCTGCGGCGCCGGGTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACcaccggcctt                                                           >  1:108621/1‑91 (MQ=0)                                                                               GTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCACCGAGATCACCCTCCTTCAGCGCGTCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC  <  1:4845198/101‑1 (MQ=1)                                                                               GTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCACCGAGATCACCCTCCTTCAGCGCGTCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC  >  2:1404810/1‑101 (MQ=1)                                              ||||||||||||||||||||||||||||||||||                                                                                                     TTATCGCCGCATGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC......................................................................................................................................  <  NC_014034/1396683‑1396639 ...............................................................................TGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCACCGAGATCACCCTCCTTCAGCGCGTCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC  <  NC_014034/1434845‑1434746 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG