New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397836 =	143 (0.940)	25 (0.170)	6/134	24.6	0.14	intergenic (+140/+1758)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
	?	NC_014034	= 1397935	152 (0.670)					intergenic (+239/+1659)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

CTGAGGTGCCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.....................................................................  <  NC_014034/1397879‑1397836 .............................................................................AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGT  <  NC_014034/1397935‑1397900                                             |||||||||||||||||||||||||||||||||                                     tgtcctTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGG              <  2:3600663/95‑1 (MQ=1)  gtcctTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGG             >  1:887402/6‑101 (MQ=1)   tcctTGCCGATTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGG            <  2:142936/97‑1 (MQ=0)    cctTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGG           <  2:2021137/98‑1 (MQ=1)     ctTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGA          <  1:4448669/99‑1 (MQ=1)      tTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAG         <  1:1713885/100‑1 (MQ=1)      tTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAG         <  2:2610744/100‑1 (MQ=1)      tTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAG         >  2:1595297/2‑101 (MQ=1)      tTGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTCCGATCCACGCCCCCGCGGGGGGAG         <  2:143840/100‑1 (MQ=0)       TGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGGGCGTCAGACAAGTTTCGATCCAAGCCCCCGCGGGGGGAGg        >  1:3989326/1‑100 (MQ=0)       TGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGC        >  1:3371662/1‑101 (MQ=1)       TGCCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTCAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGC        <  1:25827/101‑1 (MQ=0)         CCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTTAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA      >  1:1906508/1‑101 (MQ=0)         CCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA      <  2:2416091/101‑1 (MQ=1)         CCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA      >  2:3194924/1‑101 (MQ=1)         CCGAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA      <  2:3264107/101‑1 (MQ=1)          cgaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC     >  2:1582320/4‑101 (MQ=1)          cgaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC     <  1:2383835/98‑1 (MQ=1)          cgaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC     >  2:2968462/4‑101 (MQ=1)           gaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc    <  1:2086180/99‑2 (MQ=1)           gaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACc    >  1:1900234/3‑100 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACct   >  2:3749483/2‑99 (MQ=1)            aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACct   >  2:558154/2‑99 (MQ=1)             GTTTCGATCCACGCCCCCGCGGGGGGAGCGTCTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACctg  <  1:320932/101‑4 (MQ=1)             GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGAATCTTGACGTGCTGATGAGCGCGTCAGACAAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACctg  <  2:4283484/101‑4 (MQ=1)                                             |||||||||||||||||||||||||||||||||                                     CTGAGGTGCCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC.....................................................................  <  NC_014034/1397879‑1397836 .............................................................................AGTTTCGATCCACGCCCCCGCGGGGGGAGCGACTGT  <  NC_014034/1397935‑1397900 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG