New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1395964 =	157 (0.990)	79 (0.500)	18/134	17.7	0.50	intergenic (+776/‑155)	RCAP_rcc01306/RCAP_rcc01307	Cas2 family CRISPR‑associated protein/hypothetical protein
	?	NC_014034	= 1434778	NA (NA)					intergenic (‑557/‑401)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

GCAAGCGCGGATCGAGGGCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC............................................................................  <  NC_014034/1396017‑1395964 .......................................................................................CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGCTGCCCG  <  NC_014034/1434778‑1434736                                                       |||||||||||||||||||||||||||||||||                                            ggctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACG                               <  1:3183781/94‑1 (MQ=0)  gctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGC                              <  1:1035207/95‑1 (MQ=0)   ctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCC                             >  2:3875741/6‑101 (MQ=0)   ctgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCC                             >  1:2601156/6‑101 (MQ=0)    tgacCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCC                            >  2:3047091/5‑101 (MQ=0)      gcCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                          <  2:2177847/99‑1 (MQ=1)      acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                          <  1:1370893/99‑1 (MQ=1)      acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                          >  1:4097746/3‑101 (MQ=1)      acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                          <  2:4321707/99‑1 (MQ=1)      acCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCC                          >  1:2697968/3‑101 (MQ=1)       cCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCG                         <  2:756618/100‑1 (MQ=1)       cCGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCG                         >  1:441992/2‑101 (MQ=1)        CGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGC                        <  1:4381478/101‑1 (MQ=1)        CGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGC                        <  2:3666458/101‑1 (MQ=1)        CGGATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGC                        >  1:1345016/1‑101 (MQ=1)          GATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGG                      >  2:850229/1‑101 (MQ=1)          GATCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGG                      >  1:3868899/1‑101 (MQ=1)            TCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                    <  1:2507218/101‑1 (MQ=1)            TCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                    >  2:206285/1‑101 (MQ=1)            TCGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                    >  2:4425292/1‑101 (MQ=1)             CGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                   <  1:496224/101‑1 (MQ=1)             CGAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                   >  1:2700506/1‑101 (MQ=1)              gacgcCGAGTTACGATCCACGCCCCCGCGGGGGGAGCGCCCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  <  2:3349999/96‑1 (MQ=0)              GAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  >  1:4471781/1‑101 (MQ=1)              GAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  >  2:981971/1‑101 (MQ=1)              GAGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  <  1:2991329/101‑1 (MQ=1)               AGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                 <  2:340878/101‑1 (MQ=1)               AGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                 <  1:2141991/101‑1 (MQ=1)               AGGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                 <  1:2581699/101‑1 (MQ=1)                 gccggGTTTGGACCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  1:869624/96‑1 (MQ=0)                 gcCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  1:3204648/99‑1 (MQ=1)                 gcCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  1:974881/99‑1 (MQ=1)                  cCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG              <  2:3006223/100‑1 (MQ=1)                  cCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG              <  1:572720/100‑1 (MQ=1)                   CGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGA             >  2:4612903/1‑101 (MQ=1)                    GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAACGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  2:764895/101‑1 (MQ=1)                    GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  1:3860529/101‑1 (MQ=1)                    GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  2:2680248/101‑1 (MQ=1)                    GAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            >  1:2917010/1‑101 (MQ=1)                     AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa           >  2:2221824/1‑100 (MQ=1)                     AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa           <  2:1752721/101‑2 (MQ=1)                     AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa           <  1:3095857/101‑2 (MQ=1)                      GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGaaacctcgg          <  2:1332394/101‑10 (MQ=0)                       TTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagt         <  1:2267642/101‑4 (MQ=14)                       TTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagg         >  1:1424812/1‑98 (MQ=14)                        TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        >  1:218179/1‑97 (MQ=14)                        TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  1:4216720/101‑5 (MQ=14)                        TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  1:4390574/101‑5 (MQ=14)                        TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  1:1808681/101‑5 (MQ=14)                        TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        >  2:2197567/1‑97 (MQ=14)                        TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  2:1610708/101‑5 (MQ=14)                         TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  1:3940869/101‑6 (MQ=14)                         TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  2:178334/101‑6 (MQ=14)                         TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  1:165982/101‑6 (MQ=14)                         TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  1:782169/101‑6 (MQ=14)                         TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagggt       >  1:1937866/1‑96 (MQ=14)                          CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      <  1:3026687/101‑7 (MQ=17)                          CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      <  2:1455556/101‑7 (MQ=17)                          CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      <  1:1823222/101‑7 (MQ=17)                          CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      >  1:4392637/1‑95 (MQ=17)                          CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      >  1:4187166/1‑95 (MQ=17)                          CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      >  1:154476/1‑95 (MQ=17)                          CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCgtgtt      >  2:1727026/1‑96 (MQ=1)                           gacCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttg     <  1:4261340/98‑8 (MQ=12)                           GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGTGCGACagtgttg     <  1:2528256/101‑8 (MQ=12)                           GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttg     >  1:3158007/1‑94 (MQ=17)                           GATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttg     >  2:233688/1‑94 (MQ=17)                            ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    <  1:3692723/101‑9 (MQ=17)                            ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    >  2:258215/1‑93 (MQ=17)                            ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    <  2:2494299/101‑9 (MQ=17)                            ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    >  2:1419031/1‑93 (MQ=17)                            ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    >  1:4507913/1‑93 (MQ=17)                            ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    <  1:4524058/101‑9 (MQ=17)                             TCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgac   >  2:3607657/1‑92 (MQ=12)                             TCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgac   >  2:3143444/1‑92 (MQ=12)                             TCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgac   >  1:477244/1‑92 (MQ=12)                              CCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgacc  >  2:3943959/1‑91 (MQ=12)                              CCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgacc  <  1:1780407/101‑11 (MQ=12)                              CCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgacc  <  2:2164731/101‑11 (MQ=12)                                                       |||||||||||||||||||||||||||||||||                                            GCAAGCGCGGATCGAGGGCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACC............................................................................  <  NC_014034/1396017‑1395964 .......................................................................................CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGCTGCCCG  <  NC_014034/1434778‑1434736 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG