New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1396167 =	142 (0.910)	64 (0.410)	2/132	30.7	0.47	coding (49/1578 nt)	RCAP_rcc01307	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.

GTTTTTCGCCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.............................................................................  <  NC_014034/1396210‑1396167 ..............................................................................CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGCTGCCCG  <  NC_014034/1434778‑1434736                                             ||||||||||||||||||||||||||||||||||                                            gatcgagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGG                      >  2:850229/8‑101 (MQ=1) gatcgagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGG                      >  1:3868899/8‑101 (MQ=1)   tcgagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                    >  2:4425292/6‑101 (MQ=1)   tcgagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                    >  2:206285/6‑101 (MQ=1)   tcgagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGG                    <  1:2507218/96‑1 (MQ=1)    cgagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                   <  1:496224/97‑1 (MQ=1)    cgagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGG                   >  1:2700506/5‑101 (MQ=1)     gagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  >  1:4471781/4‑101 (MQ=1)     gagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  <  1:2991329/98‑1 (MQ=1)     gagGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  >  2:981971/4‑101 (MQ=1)     gaCGCCGAGTTACGATCCACGCCCCCGCGGGGGGAGCGCCCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGG                  <  2:3349999/99‑1 (MQ=0)      agGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                 <  1:2581699/99‑1 (MQ=1)      agGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                 <  1:2141991/99‑1 (MQ=1)      agGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGA                 <  2:340878/99‑1 (MQ=1)        GCCGGGTTTGGACCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  1:869624/101‑1 (MQ=0)        GCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  1:974881/101‑1 (MQ=1)        GCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  1:3204648/101‑1 (MQ=1)         CCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG              <  2:3006223/101‑1 (MQ=1)         CCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCG              <  1:572720/101‑1 (MQ=1)          cgaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGA             >  2:4612903/4‑101 (MQ=1)           gaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAACGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  2:764895/99‑1 (MQ=1)           gaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            >  1:2917010/3‑101 (MQ=1)           gaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  1:3860529/99‑1 (MQ=1)           gaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  2:2680248/99‑1 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa           <  1:3095857/100‑2 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa           >  2:2221824/2‑100 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACa           <  2:1752721/100‑2 (MQ=1)             GTTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGaaacctcgg          <  2:1332394/101‑10 (MQ=0)              TTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagt         <  1:2267642/101‑4 (MQ=14)              TTTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagg         >  1:1424812/1‑98 (MQ=14)               TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  1:1808681/101‑5 (MQ=14)               TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  1:4390574/101‑5 (MQ=14)               TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  1:4216720/101‑5 (MQ=14)               TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        >  1:218179/1‑97 (MQ=14)               TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        <  2:1610708/101‑5 (MQ=14)               TTCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtg        >  2:2197567/1‑97 (MQ=14)                TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  1:165982/101‑6 (MQ=14)                TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  1:782169/101‑6 (MQ=14)                TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  1:3940869/101‑6 (MQ=14)                TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgt       <  2:178334/101‑6 (MQ=14)                TCGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagggt       >  1:1937866/1‑96 (MQ=14)                 CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      >  1:154476/1‑95 (MQ=17)                 CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      <  1:1823222/101‑7 (MQ=17)                 CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      <  1:3026687/101‑7 (MQ=17)                 CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      >  1:4392637/1‑95 (MQ=17)                 CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      <  2:1455556/101‑7 (MQ=17)                 CGATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgtt      >  1:4187166/1‑95 (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    >  1:4507913/1‑93 (MQ=17)                   ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    <  1:4524058/101‑9 (MQ=17)                   ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    >  2:1419031/1‑93 (MQ=17)                   ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    >  2:258215/1‑93 (MQ=17)                   ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    <  2:2494299/101‑9 (MQ=17)                   ATCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttga    <  1:3692723/101‑9 (MQ=17)                    TCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgac   >  2:3143444/1‑92 (MQ=12)                    TCCACGCCCCCGCGGGGGGAGCGACCGCGCAGACAAAGATCCGGCGCGGCGCGCGCCAGCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACagtgttgac   >  2:3607657/1‑92 (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)                                             ||||||||||||||||||||||||||||||||||                                            GTTTTTCGCCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.............................................................................  <  NC_014034/1396210‑1396167 ..............................................................................CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACCAGCTGCCCG  <  NC_014034/1434778‑1434736 Base quality scores:  ATCG  < 3 ≤  ATCG  < 19 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG