New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	0 (0.000)	75 (0.360)	28/176	17.8	0.43	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	2808467 =	199 (0.840)					intergenic (+22/+132)	pyrD2/acsA2	dihydroorotate oxidase/acetate‑‑CoA ligase
Rejected: Position hash score below cutoff.

CGCAATGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGT...................................................................................................  <  NC_014034/1608162‑1608051 ....................................................................................................AGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTGCGCCAAGAAAAAGCACAGACTTTTGCCCGTTCACCCTGGCGCAAATCTCCCGGGGGGAGAGTGGCGCA  >  NC_014034/2808467‑2808565                                                                                                                                                                                                                                  GCCGTGGCCAGACCCGAGCGCCCGATCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTT                                                                                                    <  2:727648/101‑1 (MQ=1)             GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTT                                                                                                    >  1:3867113/1‑101 (MQ=1)               CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTC                                                                                                  <  2:3866828/101‑1 (MQ=1)               CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTC                                                                                                  <  2:3356485/101‑1 (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                                                                                               <  1:168321/101‑1 (MQ=1)                  GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACA                                                                                               >  1:3640183/1‑101 (MQ=1)                   GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACAC                                                                                              >  2:2725233/1‑101 (MQ=1)                   GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACAC                                                                                              >  2:2902325/1‑101 (MQ=1)                   GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACAC                                                                                              <  1:226250/101‑1 (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                                                                                           >  2:3921231/1‑101 (MQ=1)                      AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCC                                                                                           <  1:3173785/101‑1 (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                                                                                     >  2:1235654/1‑101 (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.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                                                                                  <  2:4477400/101‑1 (MQ=1)                               CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                  <  1:3905702/101‑1 (MQ=1)                               CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                  <  1:2870174/101‑1 (MQ=1)                               CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                  >  1:627014/1‑101 (MQ=1)                               CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                  <  1:2439124/101‑1 (MQ=1)                               CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCC                                                                                  <  2:3357764/101‑1 (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                                                                          >  1:905454/1‑97 (MQ=32)                                       CCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgata                                                                          <  1:2131916/101‑5 (MQ=32)                                        CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  2:810195/101‑6 (MQ=32)                                        CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  2:868106/101‑6 (MQ=32)                                        CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  1:2724164/101‑6 (MQ=32)                                        CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  1:4478360/101‑6 (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                                                                       <  1:1287858/101‑1 (MQ=32)                                          CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                       <  1:4121184/101‑1 (MQ=32)                                          CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                       >  2:1578016/1‑101 (MQ=32)                                          CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                       <  2:3601356/101‑1 (MQ=32)                                           AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTG                                                                      <  1:3894216/101‑1 (MQ=32)                                           AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTG                                                                      <  1:1781193/101‑1 (MQ=32)                                           AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTG                                                                      <  1:1495424/101‑1 (MQ=32)                                            GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGa                                                                     >  2:4629107/1‑100 (MQ=33)                                            GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTAACACCCCCGCACCCCCGTGGGATATTTGa                                                                     <  1:1344187/101‑2 (MQ=18)                                             CACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGag                                                                    <  2:1016810/101‑3 (MQ=34)                                               CCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGaggc                                                                  <  1:3344158/101‑5 (MQ=37)                                                CGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGaggca                                                                 <  1:2009656/101‑6 (MQ=38)                                                CGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGaggca                                                                 <  1:1431700/101‑6 (MQ=38)                                                                                                                                                                                                                      CGCAATGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTG.CGGGGGT...................................................................................................  <  NC_014034/1608162‑1608051 ....................................................................................................AGCTG.CGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTGCGCCAAGAAAAAGCACAGACTTTTGCCCGTTCACCCTGGCGCAAATCTCCCGGGGGGAGAGTGGCGCA  >  NC_014034/2808467‑2808565 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 27 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG