New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1395964 =	140 (0.990)	59 (0.420)	20/134	13.3	0.29	intergenic (+776/‑155)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	= 1396470	152 (0.720)					coding (352/1578 nt)	RCAP_rcc01307	hypothetical protein
Rejected: Position hash score below cutoff.

GGCAAGCGCGGATCGAGGGCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC..........................................................................  <  NC_014034/1396018‑1395964 ........................................................................................CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCCGTGG  <  NC_014034/1396470‑1396430                                                        |||||||||||||||||||||||||||||||||                                          aggctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCAC                              <  1:1050881/93‑1 (MQ=0) aggctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCAC                              <  1:3153321/93‑1 (MQ=0) aggctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCAC                              <  2:394044/93‑1 (MQ=0)  ggctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACG                             >  1:4063541/8‑101 (MQ=0)  ggctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACG                             <  2:162503/94‑1 (MQ=0)  ggctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACG                             <  2:4070763/94‑1 (MQ=0)    ctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCC                           <  2:3797189/96‑1 (MQ=0)     tgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCC                          <  1:3034532/97‑1 (MQ=0)     tgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCC                          >  1:2645811/5‑101 (MQ=0)     tgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCC                          >  2:509578/5‑101 (MQ=0)     tgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCC                          >  2:670451/5‑101 (MQ=0)     tgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCC                          <  1:134714/97‑1 (MQ=0)     tgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCC                          >  2:784169/5‑101 (MQ=0)      gacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCC                         >  2:2484682/4‑101 (MQ=0)       acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                        <  2:3625177/99‑1 (MQ=1)       acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                        <  2:3342362/99‑1 (MQ=1)       acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                        <  2:2989341/99‑1 (MQ=1)       acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                        <  1:3701041/99‑1 (MQ=1)        cCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCGGGCTCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCG                       >  1:3618795/2‑101 (MQ=0)        cCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCG                       <  1:3309988/100‑1 (MQ=1)         CGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGC                      >  2:188601/1‑101 (MQ=1)          GGACCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCG                     >  1:3258447/1‑101 (MQ=0)           GATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGATTCGATCCACGCCCCCGCGG                    >  2:1185993/1‑101 (MQ=0)             TCGAGGCCGAGTTTCGATCCGCGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                  <  2:471760/101‑1 (MQ=0)              CGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGatc                 <  2:1143223/101‑4 (MQ=0)              CGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                 >  2:1390535/1‑101 (MQ=1)              CGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                 >  2:798709/1‑101 (MQ=1)              CGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                 <  1:3950620/101‑1 (MQ=1)              CGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                 >  1:1030820/1‑101 (MQ=1)               nAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCNGNGGn                >  1:894724/2‑100 (MQ=0)               GAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                <  2:994974/101‑1 (MQ=1)               GAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                <  1:4230925/101‑1 (MQ=1)               GAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                >  1:1551679/1‑101 (MQ=1)               GAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                >  1:1972157/1‑101 (MQ=1)                AGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGg               >  1:1246585/1‑100 (MQ=1)                AGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA               <  1:3920103/101‑1 (MQ=1)                AGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA               <  2:505930/101‑1 (MQ=1)                AGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA               <  1:3196182/101‑1 (MQ=1)                 ggcCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAG              <  1:1390635/98‑1 (MQ=1)                 ggcCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAG              <  2:501510/98‑1 (MQ=1)                  gcCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC             <  1:3905791/99‑1 (MQ=1)                  gcCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC             <  2:3038203/99‑1 (MQ=1)                   cCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG            <  1:1551124/100‑1 (MQ=1)                    CGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGA           >  1:3387187/1‑101 (MQ=1)                    CGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGA           <  1:991203/101‑1 (MQ=1)                      AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa         >  2:3726950/1‑100 (MQ=1)                      AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa         <  1:1676223/101‑2 (MQ=1)                      AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa         >  2:2848824/1‑100 (MQ=1)                      AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa         >  2:2383205/1‑100 (MQ=1)                         TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg      <  2:3703197/101‑5 (MQ=1)                         TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg      <  2:822815/101‑5 (MQ=1)                          TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt     <  2:3598272/101‑6 (MQ=1)                           CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt    >  2:3375370/1‑95 (MQ=0)                           CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtctt    <  1:2420254/101‑7 (MQ=0)                            GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGGGCGACagagttg   >  1:2149614/1‑94 (MQ=0)                            GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttg   >  2:2522771/1‑94 (MQ=0)                            GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttg   >  1:3872827/1‑94 (MQ=0)                            GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttg   >  2:2465886/1‑94 (MQ=0)                             ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga  <  2:3599946/101‑9 (MQ=0)                                                        |||||||||||||||||||||||||||||||||                                          GGCAAGCGCGGATCGAGGGCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC..........................................................................  <  NC_014034/1396018‑1395964 ........................................................................................CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCCGTGG  <  NC_014034/1396470‑1396430 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG