New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397836 =	155 (0.950)	45 (0.270)	11/138	22.8	0.22	intergenic (+140/+1758)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
	?	NC_014034	= 1434848	169 (0.710)					intergenic (‑627/‑331)	RCAP_rcc01334/RCAP_rcc01335	hypothetical protein/Fis family GAF modulated sigma54 specific transcriptional regulator
Rejected: Position hash score below cutoff.

GGGCTGAGGTGCCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC............................................................................  <  NC_014034/1397882‑1397836 ..............................................................................CCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCA  <  NC_014034/1434848‑1434804                                                |||||||||||||||||||||||||||||||                                              tccaagacGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCG                        >  2:4500142/9‑101 (MQ=0) tccaagacGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCG                        <  1:3716553/93‑1 (MQ=0)  ccaagacGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGC                       >  2:2212052/8‑101 (MQ=0)  ccaagacGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGC                       <  1:4053677/94‑1 (MQ=0)   caaGAGGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCG                      <  1:2515544/98‑1 (MQ=0)    aagacGTGGCGGTTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGG                     <  2:3162265/96‑1 (MQ=0)     agacGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGG                    >  2:51778/5‑101 (MQ=0)     agacGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGG                    <  2:355731/97‑1 (MQ=0)      gacGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGG                   <  1:421990/98‑1 (MQ=0)       acGTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGG                  <  2:938021/99‑1 (MQ=1)        cGTGGCGGGTTTCGATCCACGCCCCCCCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGG                 <  1:3922382/100‑1 (MQ=0)         GTGGCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGA                <  2:1017286/101‑1 (MQ=1)         GTGGCGGGTTTCGATCCACCCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACCCTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGA                <  2:3942793/101‑1 (MQ=0)          tggCGGTTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAG               <  2:1186824/98‑1 (MQ=0)          gggCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAG               <  2:363162/98‑1 (MQ=1)           ggCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGC              >  1:2911496/3‑101 (MQ=1)           ggCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGC              >  2:346236/3‑101 (MQ=1)           ggCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGC              <  2:2959887/99‑1 (MQ=1)            gCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGTAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCG             <  2:1081152/100‑1 (MQ=1)            gCGGGTTTCGATCCACGCCCCCGCGGCGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCG             <  1:3919459/100‑1 (MQ=1)              gtgttggGATCCCCGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC           <  2:3204231/94‑1 (MQ=0)              GGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAACCCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC           <  2:2471955/101‑1 (MQ=1)              GGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC           <  2:4608724/101‑1 (MQ=1)              GGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGAGGGGAGCGAC           <  1:149586/101‑1 (MQ=1)               GGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg          <  2:472197/101‑2 (MQ=1)               GGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg          >  2:2302311/1‑100 (MQ=1)               GGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg          >  2:2549532/1‑100 (MQ=1)                GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgc         <  2:171963/101‑3 (MQ=1)                 TTTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgca        >  2:1034116/1‑98 (MQ=1)                 TTTCGATCCACCCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgca        <  2:1783993/101‑4 (MQ=1)                  TTCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaa       <  2:2149569/101‑5 (MQ=1)                   TCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaac      <  2:1265337/101‑6 (MQ=1)                   TCGATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaac      >  1:3430769/1‑96 (MQ=1)                    CGACCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaacc     <  2:439236/101‑7 (MQ=0)                     GATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccg    >  1:2026338/1‑94 (MQ=1)                      acCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgc   <  2:4362149/99‑9 (MQ=0)                      ATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgc   >  2:1370454/1‑93 (MQ=1)                      ATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgc   >  2:1135072/1‑93 (MQ=1)                      ATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgc   >  2:685449/1‑93 (MQ=1)                      ATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgc   >  2:826403/1‑93 (MQ=1)                      ATCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgc   >  2:24096/1‑93 (MQ=1)                       TCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgcg  <  1:3768479/101‑10 (MQ=0)                       TCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgcg  <  2:4593709/101‑10 (MQ=0)                       TCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgcg  >  2:1040619/1‑92 (MQ=0)                       TCCACGCCCCCGCGGGGGGAGCGACGCCGCTGGAAAACCTGACACTGCCGCCATAGCCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgcaaccgcg  >  2:2701087/1‑92 (MQ=0)                                                |||||||||||||||||||||||||||||||                                              GGGCTGAGGTGCCGGGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC............................................................................  <  NC_014034/1397882‑1397836 ..............................................................................CCATGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAAGGCGCCA  <  NC_014034/1434848‑1434804 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 23 ≤  ATCG  < 32 ≤  ATCG  < 38 ≤  ATCG