New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1397166 =	149 (0.910)	42 (0.260)	11/134	17.1	0.21	coding (1048/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	= 1397867	163 (0.670)					intergenic (+171/+1727)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

CGTGGCAGACACGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG.............................................................................  <  NC_014034/1397210‑1397166 ..............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGA  <  NC_014034/1397867‑1397824                                              |||||||||||||||||||||||||||||||||                                             ggtcttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGG                       >  1:2242726/8‑101 (MQ=0) ggtcttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGG                       >  2:2159164/8‑101 (MQ=0)   tcttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGG                     >  1:1663391/6‑101 (MQ=0)    cttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGG                    >  1:4959908/5‑101 (MQ=0)    cttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGG                    >  2:4315229/5‑101 (MQ=0)    cttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGG                    >  2:559775/5‑101 (MQ=0)     ttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGg                   >  1:2141492/4‑100 (MQ=0)     ttcGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGg                   >  2:4572235/4‑100 (MQ=0)       cgcccCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGC                 <  1:1579828/96‑1 (MQ=1)       cGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGC                 >  2:4884037/2‑101 (MQ=1)       cGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGC                 >  1:4200446/2‑101 (MQ=1)       cGACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGC                 >  2:1481213/2‑101 (MQ=1)        ccccCGTTTCGATCCACGCCCCCGGGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCG                <  2:2184247/97‑1 (MQ=0)        GACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCG                >  1:2544229/1‑101 (MQ=1)        GACCCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCG                >  2:2562468/1‑101 (MQ=1)         cccCGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGA               <  1:2073811/98‑1 (MQ=0)          ccCGTTTCGACCCCCGCCCCCGGGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC              <  1:1830242/99‑1 (MQ=0)           cCGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACA             >  1:631125/2‑101 (MQ=1)            CGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAT            >  2:3997987/1‑101 (MQ=1)            CGTTTCGACCCCCGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACAT            <  1:2967903/101‑1 (MQ=0)             GTTTCGATCCACGCCCCCGGGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATc           <  1:4187055/101‑2 (MQ=1)              TTTCGATCCACGCCCCCGCGGGGGGAGCGACAATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCTCGCGGGGGGAGCGACATcc          >  1:2841709/1‑99 (MQ=0)              TTTCGACCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcc          <  2:328716/101‑3 (MQ=1)               TTCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcct         >  1:4619179/1‑98 (MQ=1)                TCGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctg        >  2:559334/1‑97 (MQ=1)                 CGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgt       >  1:648705/1‑96 (MQ=1)                 CGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgt       >  2:4201886/1‑96 (MQ=1)                 CGATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgt       >  1:2597771/1‑96 (MQ=1)                 CGACCCCCGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgt       <  1:2152197/101‑6 (MQ=0)                 CGACCCACCCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgt       <  2:584446/101‑6 (MQ=0)                  GATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgtt      >  1:3547305/1‑95 (MQ=0)                   ATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGGGCGACATcctgttc     >  1:3427133/1‑94 (MQ=0)                   ATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttc     >  2:917367/1‑94 (MQ=0)                   ATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttc     >  1:4626638/1‑94 (MQ=0)                   ATCCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttc     >  1:310441/1‑94 (MQ=0)                     CCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttcca   >  1:965075/1‑92 (MQ=0)                     CCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttcca   >  1:288028/1‑92 (MQ=0)                     CCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttcca   >  2:910089/1‑92 (MQ=0)                     CCACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttcca   >  1:1426925/1‑92 (MQ=0)                      CACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttccag  >  2:2083432/1‑91 (MQ=0)                      CACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttccag  >  1:979843/1‑91 (MQ=0)                      CACGCCCCCGCGGGGGGAGCGACGATAGCCCGCCGTGAACTCGGTCGAGCCAGCATAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACATcctgttccag  >  1:4791107/1‑91 (MQ=0)                                              |||||||||||||||||||||||||||||||||                                             CGTGGCAGACACGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG.............................................................................  <  NC_014034/1397210‑1397166 ..............................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACATGGCGATGCGA  <  NC_014034/1397867‑1397824 Base quality scores:  ATCG  < 3 ≤  ATCG  < 18 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG