New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	32 (0.080)	73 (0.170)	5/186	37.9	0.22	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	3504133 =	499 (1.090)					intergenic (‑26/+57)	recO/RCAP_rcc03309	DNA repair protein RecO/hypothetical protein
Rejected: Position hash score below cutoff.

TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ....................................................................................................CGGGGGTTTTGCACCCCCGGGCCCCCGCAGGATATTTGAGGCAAGATAAAAGCGAAAGCCGGGGTCAGTCTTTCAGTCCGTCTTCATCCAGAAGCGTGCGGCCGTGC  >  NC_014034/3504133‑3504232                                                                                                                                                                                                                        cCCGTGGCCAGACCCGGGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCTTATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     <  2:2623039/100‑1 (MQ=0)        GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     >  2:2721009/1‑101 (MQ=1)        GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     <  2:8715144/101‑1 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    >  2:8355084/1‑101 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    <  1:7967682/101‑1 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    >  2:5553826/1‑101 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    >  2:2375260/1‑101 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    <  1:3161962/101‑1 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTT                                                                                                    >  1:8492867/1‑101 (MQ=1)          caTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  1:7764935/99‑2 (MQ=1)          CGTGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  2:8453108/101‑2 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  2:2845085/101‑2 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   >  1:4346681/1‑100 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  2:6912319/101‑2 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  1:2414190/101‑2 (MQ=1)          CGTGCCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  2:833342/101‑2 (MQ=0)           GTGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:5980665/101‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTga                                                                                                  >  1:5005165/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:6673518/101‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  1:3295873/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:6174928/101‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  1:90511/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  1:2590498/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:396320/101‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTca                                                                                                  >  2:2303032/1‑99 (MQ=1)           GTGCCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGCCCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:1611243/101‑3 (MQ=0)            gGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 <  2:585246/100‑4 (MQ=1)            TGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 <  1:8739964/101‑4 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 >  1:8438402/1‑98 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 <  1:329942/101‑4 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 >  2:2605819/1‑98 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 >  2:7684610/1‑98 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 <  2:1959626/101‑4 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTcac                                                                                                 >  2:5961566/1‑98 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTCCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 >  1:6334312/1‑98 (MQ=1)             GGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcaca                                                                                                <  1:286207/101‑5 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcaca                                                                                                >  2:7917707/1‑97 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcaca                                                                                                >  1:1598824/1‑97 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               <  2:437445/101‑6 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               <  1:1375680/101‑6 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               <  1:8369206/101‑6 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               <  2:1782612/101‑6 (MQ=1)               CCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACC                                                                                              >  1:8657939/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             >  2:6846105/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             >  1:4799591/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGCTTCACACCC                                                                                             >  2:4680241/1‑101 (MQ=1)                 agcCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                            <  2:1501442/98‑1 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                            >  1:2189250/1‑101 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                            <  1:6851840/101‑1 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                            >  2:563716/1‑101 (MQ=1)                  gcCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  2:1411669/99‑1 (MQ=1)                  GACCCGAGCGCCCGAGCNCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  2:1063702/101‑1 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           >  1:7675085/1‑101 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  1:2562724/101‑1 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  1:2605901/101‑1 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  1:3811847/101‑1 (MQ=1)                   cCCCGAGCGCCGGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  2:1857836/100‑1 (MQ=1)                   cCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  1:5484674/100‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  2:6946223/101‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          >  2:4089073/1‑101 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  2:1015304/101‑1 (MQ=1)                    CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGc                                                                                         <  1:2229208/101‑2 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcac                                                                                       <  1:52258/101‑4 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcac                                                                                       <  2:6049906/101‑4 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcac                                                                                       <  2:2263853/101‑4 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcac                                                                                       <  2:8294747/101‑4 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      >  1:5233423/1‑97 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      >  1:6059659/1‑97 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      <  1:2687518/101‑5 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      >  2:5541505/1‑97 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      >  1:7508684/1‑97 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      <  2:3457418/101‑5 (MQ=1)                        AGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcaccc                                                                                     <  1:2130583/101‑6 (MQ=1)                                                                                                                                                                                                                 TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ....................................................................................................CGGGGGTTTTGCACCCCCGGGCCCCCGCAGGATATTTGAGGCAAGATAAAAGCGAAAGCCGGGGTCAGTCTTTCAGTCCGTCTTCATCCAGAAGCGTGCGGCCGTGC  >  NC_014034/3504133‑3504232 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 41 ≤  ATCG