New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	0 (0.000)	73 (0.330)	28/184	18.7	0.50	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	= 1820392	146 (0.610)					intergenic (+83/‑103)	RCAP_rcc01683/RCAP_rcc01684	terminase‑like family protein/HK97 family phage portal protein
Rejected: Position hash score below cutoff.

TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ...................................................................................................G.CGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTTCACCAAGAAAAAACACGCAGCTTTTTCCTGGTCCAAATACGCCCTTGCGCGCTCAAAGCCCGCGCACCT  <  NC_014034/1820392‑1820293                                                                                                                                                                                                                         GCCGTGGCCAGACCCGAGCGCCCGATCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTT                                                                                                     <  2:727648/101‑1 (MQ=1)        GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTT                                                                                                     >  1:3867113/1‑101 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTC                                                                                                   <  2:3356485/101‑1 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTC                                                                                                   <  2:3866828/101‑1 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAACTG.CGGGGGTTgc                                                                                                   >  2:834355/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATCTCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGCGGTTCCA                                                                                                  >  2:4389953/1‑101 (MQ=0)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCA                                                                                                  >  1:1525172/1‑101 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCA                                                                                                  <  2:4602531/101‑1 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCA                                                                                                  >  1:2720724/1‑101 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCA                                                                                                  <  1:645147/101‑1 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACA                                                                                                >  1:3640183/1‑101 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACA                                                                                                <  1:168321/101‑1 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACAC                                                                                               <  1:226250/101‑1 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACAC                                                                                               >  2:2902325/1‑101 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACAC                                                                                               >  2:2725233/1‑101 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACAC                                                                                               >  2:4478065/1‑101 (MQ=1)               CCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACC                                                                                              >  1:4424186/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCC                                                                                             >  2:4399020/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCC                                                                                             >  1:175157/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCC                                                                                             <  2:1996607/101‑1 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCC                                                                                            <  1:3173785/101‑1 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCC                                                                                            >  2:3921231/1‑101 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCC                                                                                           >  1:2888433/1‑101 (MQ=1)                   cCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCG                                                                                          <  1:1899089/100‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCG                                                                                          <  1:1758146/101‑1 (MQ=1)                    CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGC                                                                                         <  2:4423894/101‑1 (MQ=1)                    CCCGAGCCCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGC                                                                                         <  2:548541/101‑1 (MQ=1)                     CCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCCGGGGGTTTCACCCCCCCcc                                                                                         >  1:3452477/1‑99 (MQ=2)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCAC                                                                                       <  2:1863904/101‑1 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCAC                                                                                       <  1:4122887/101‑1 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACC                                                                                      <  2:1525063/101‑1 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACC                                                                                      <  1:3406527/101‑1 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACC                                                                                      <  2:704335/101‑1 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACC                                                                                      >  2:1235654/1‑101 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGGTTCACACCCCCGCACC                                                                                      >  1:3601624/1‑101 (MQ=1)                        AGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCC                                                                                     >  2:4384047/1‑101 (MQ=1)                         gccCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCC                                                                                    <  2:3393370/98‑1 (MQ=1)                         GCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCC                                                                                    <  2:3969419/101‑1 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                   <  2:3357764/101‑1 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                   >  1:627014/1‑101 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                   <  2:4477400/101‑1 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                   <  1:3905702/101‑1 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                   <  1:2870174/101‑1 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                   <  1:2439124/101‑1 (MQ=1)                            CCCGAGCCCCAGCCCCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACCCCCCCGCACCCCCGT                                                                                 <  2:3876767/101‑1 (MQ=0)                            CCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGT                                                                                 <  1:3494316/101‑1 (MQ=1)                            CCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGT                                                                                 <  1:239311/101‑1 (MQ=1)                             CCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTG                                                                                <  2:3770833/101‑1 (MQ=1)                             CCGAGCCCCAGCACCGCCACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTG                                                                                <  2:4189264/101‑1 (MQ=1)                              CGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGG                                                                               <  1:4266832/101‑1 (MQ=1)                               GAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGg                                                                              <  1:3323614/101‑2 (MQ=11)                               GAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGg                                                                              <  1:256564/101‑2 (MQ=11)                                 GCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgat                                                                            <  2:59282/101‑4 (MQ=32)                                  CCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgata                                                                           <  1:2131916/101‑5 (MQ=32)                                  CCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgata                                                                           >  1:905454/1‑97 (MQ=32)                                   CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  2:810195/101‑6 (MQ=32)                                   CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  2:868106/101‑6 (MQ=32)                                   CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  1:4478360/101‑6 (MQ=32)                                   CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  1:2724164/101‑6 (MQ=32)                                   CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGGTTCACACCCCCGCACCCCCGTGGgatat                                                                          >  1:3958740/1‑96 (MQ=17)                                    CCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATT                                                                         >  2:1294949/1‑101 (MQ=32)                                    CCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATT                                                                         <  2:1270484/101‑1 (MQ=32)                                     CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                        <  2:3601356/101‑1 (MQ=32)                                     CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                        >  2:1578016/1‑101 (MQ=32)                                     CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                        <  1:4121184/101‑1 (MQ=32)                                     CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                        <  1:1287858/101‑1 (MQ=32)                                      AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTg                                                                       <  1:3894216/101‑2 (MQ=32)                                      AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTg                                                                       <  1:1781193/101‑2 (MQ=32)                                      AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTg                                                                       <  1:1495424/101‑2 (MQ=32)                                       GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTga                                                                      >  2:4629107/1‑99 (MQ=33)                                       GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTAACACCCCCGCACCCCCGTGGGATATTTga                                                                      <  1:1344187/101‑3 (MQ=18)                                        CACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgag                                                                     <  2:1016810/101‑4 (MQ=34)                                          CCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgaggc                                                                   <  1:3344158/101‑6 (MQ=37)                                                                                                                                                                                                                  TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ...................................................................................................G.CGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTTCACCAAGAAAAAACACGCAGCTTTTTCCTGGTCCAAATACGCCCTTGCGCGCTCAAAGCCCGCGCACCT  <  NC_014034/1820392‑1820293 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG