New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1396902 =	121 (0.870)	40 (0.290)	3/132	24.9	0.23	coding (784/1578 nt)	RCAP_rcc01307	hypothetical protein
	?	NC_014034	= 1398002	148 (0.700)					intergenic (+306/+1592)	RCAP_rcc01307/RCAP_rcc01309	hypothetical protein/IS66 family transposase
Rejected: Position hash score below cutoff.

TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGCAGGCGGAAGCCGATGCGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG............................................................................  <  NC_014034/1396999‑1396902 ....................................................................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTTTTGAAGGT  <  NC_014034/1398002‑1397961                                                                                                   ||||||||||||||||||||||||||||||||||                                           TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGCAGGCGGAAGCCGATGCGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGtc                                                                           <  2:1579462/101‑3 (MQ=1)  TTCGATCCACGCCCCCGCGGGGGGAGCGACCACGCAGGCGGAAGCCGATGCGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGGCACGGctg                                                                          >  2:3282143/1‑98 (MQ=0)                                                   catggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCG                         <  1:4051422/96‑1 (MQ=0)                                                    atggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGC                        >  2:2343587/5‑101 (MQ=2)                                                    atggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGC                        >  2:2446692/5‑101 (MQ=2)                                                      ggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCCCGG                      >  2:964770/3‑101 (MQ=0)                                                      ggCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCCCGG                      >  1:1225931/3‑101 (MQ=0)                                                       gCGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGG                     <  1:434030/100‑1 (MQ=0)                                                        CGCGCCCGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGG                    <  2:4119558/101‑1 (MQ=2)                                                        CGCGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGCTCCACGCCCCCGCGGGG                    >  2:303094/1‑101 (MQ=0)                                                          CGCACGCGGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGG                  <  1:444584/101‑1 (MQ=1)                                                          CGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCTCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGG                  >  1:3571313/1‑101 (MQ=2)                                                          CGCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGG                  >  2:1795645/1‑101 (MQ=11)                                                           gcccgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGA                 <  1:812489/94‑1 (MQ=11)                                                           ccgcggTGTTTCGATCCCCGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGA                 <  2:3193246/95‑1 (MQ=0)                                                           GCACGCAGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGg                 >  2:4135168/1‑100 (MQ=11)                                                            cacgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGgg                >  1:1170059/7‑99 (MQ=11)                                                            cacgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAG                <  2:1986429/95‑1 (MQ=11)                                                            cacgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAG                <  2:1964467/95‑1 (MQ=11)                                                             ccgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGC               <  2:3956885/96‑1 (MQ=11)                                                             acgcaGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGC               >  2:449355/6‑101 (MQ=11)                                                               gcaGTTTCGATCCACGCTCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGA             <  2:3799775/98‑1 (MQ=1)                                                                caGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGAC            <  1:418309/99‑1 (MQ=1)                                                                 aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGGGCGACg           >  1:1248864/2‑100 (MQ=1)                                                                 aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg           >  1:444287/2‑100 (MQ=1)                                                                 aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg           >  2:499947/2‑100 (MQ=1)                                                                 aGTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACg           >  1:2647483/2‑100 (MQ=1)                                                                  GTTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGAGAGCGACgt          <  2:1220508/101‑3 (MQ=1)                                                                  GTTTCGAGCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgt          <  2:721106/101‑3 (MQ=1)                                                                   TTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtg         <  2:2396321/101‑4 (MQ=1)                                                                   TTTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtg         >  2:26960/1‑98 (MQ=1)                                                                    TTCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgc        <  1:1743777/101‑5 (MQ=1)                                                                     TCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcg       <  1:1951001/101‑6 (MQ=1)                                                                     TCGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcg       >  2:1713020/1‑96 (MQ=1)                                                                      CGATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcga      <  1:3733577/101‑7 (MQ=1)                                                                       GATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgag     >  1:2900958/1‑94 (MQ=0)                                                                        ATCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgagg    >  2:404372/1‑93 (MQ=0)                                                                         TCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgaggg   >  1:1796616/1‑92 (MQ=0)                                                                         TCCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgaggg   >  2:212854/1‑92 (MQ=0)                                                                          CCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgagggc  >  1:599133/1‑91 (MQ=0)                                                                          CCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgagggc  >  2:959109/1‑91 (MQ=0)                                                                          CCACGCCCCCGCGGGGGGAGCGACGGGCGGGTCCGTCAGCCATAGGCCCGCGCCGCATTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACgtgcgagggc  <  2:988126/101‑11 (MQ=0)                                                                                                   ||||||||||||||||||||||||||||||||||                                           TTTCGATCCACGCCCCCGCGGGGGGAGCGACCACGCAGGCGGAAGCCGATGCGGCCGCGCAGGCTGTTTCGATCCACGCCCCCGCGGGGGGAGCGACG............................................................................  <  NC_014034/1396999‑1396902 ....................................................................................................................................GTTTCGATCCACGCCCCCGCGGGGGGAGCGACTTTTGAAGGT  <  NC_014034/1398002‑1397961 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 23 ≤  ATCG  < 32 ≤  ATCG  < 39 ≤  ATCG