New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	0 (0.000)	55 (0.300)	25/176	15.4	0.36	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	2808467 =	196 (0.930)					intergenic (+22/+132)	pyrD2/acsA2	dihydroorotate oxidase/acetate‑‑CoA ligase
Rejected: Position hash score below cutoff.

CGCAATGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT...................................................................................................  <  NC_014034/1608162‑1608051 ....................................................................................................AGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTGCGCCAAGAAAAAGCACAGACTTTTGCCCGTTCACCCTGGCGCAAATCTCCCGGGGGGAGAGTGGCGCA  >  NC_014034/2808467‑2808565                                                                                                                                                                                                                                 GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                    <  1:680324/101‑1 (MQ=1)             GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                    <  1:2271214/101‑1 (MQ=1)              gCGTGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                   <  2:2076941/100‑1 (MQ=1)              CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                   <  2:1327123/101‑1 (MQ=1)              CCGTGCCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                   <  2:164894/101‑1 (MQ=1)               CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTC                                                                                                  <  1:861350/101‑1 (MQ=1)               CGTGACCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTC                                                                                                  <  2:1755565/101‑1 (MQ=1)                 TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCAC                                                                                                >  2:3979325/1‑101 (MQ=1)                  GGCCAGACCCGAGCGCCCGAGCCCCAGCACCCCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCAaa                                                                                               >  1:3779180/1‑99 (MQ=1)                     CAGACCCGAGCTCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGGCCTCCGTAAGCTGCGGGGGTTTCACCCCC                                                                                            <  2:3586121/101‑1 (MQ=0)                     CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGGTCACACCC                                                                                            >  1:127549/1‑101 (MQ=0)                      AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                           <  2:1841784/101‑1 (MQ=1)                      AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                           <  2:2093631/101‑1 (MQ=1)                       gcCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                          <  2:3723554/99‑1 (MQ=1)                       GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                          <  1:1008254/101‑1 (MQ=1)                        ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                         <  2:182636/101‑1 (MQ=1)                         CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGC                                                                                        <  2:2229140/101‑1 (MQ=1)                         CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGC                                                                                        <  1:1762847/101‑1 (MQ=1)                         CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGC                                                                                        <  2:4196751/101‑1 (MQ=1)                          CCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCA                                                                                       >  2:2788549/1‑101 (MQ=1)                          CCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCA                                                                                       <  2:3432303/101‑1 (MQ=1)                           CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCAC                                                                                      >  2:166609/1‑101 (MQ=1)                           CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCAC                                                                                      <  2:587209/101‑1 (MQ=1)                            GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACCCCCCCACC                                                                                     >  1:2157515/1‑101 (MQ=0)                            GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGGTCACACCCCCGCACC                                                                                     >  2:3757019/1‑101 (MQ=0)                             AGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCC                                                                                    >  2:368002/1‑101 (MQ=1)                             AGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACCCCCGCACCC                                                                                    >  1:3798545/1‑101 (MQ=1)                              GCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCC                                                                                   <  1:664980/101‑1 (MQ=1)                              GCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCC                                                                                   >  2:3837594/1‑101 (MQ=1)                               CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCC                                                                                  <  2:2588916/101‑1 (MQ=1)                                GCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCG                                                                                 <  2:2226507/101‑1 (MQ=1)                                 CCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGT                                                                                <  1:369455/101‑1 (MQ=1)                                  CCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTG                                                                               <  1:3903690/101‑1 (MQ=1)                                   CGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGG                                                                              <  1:3511562/101‑1 (MQ=1)                                   CGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGG                                                                              <  2:2120772/101‑1 (MQ=1)                                     AGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGga                                                                            >  1:3235243/1‑99 (MQ=31)                                       CCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgata                                                                          <  2:2821397/101‑5 (MQ=32)                                        CCCAGCACCGCGAGGCGCGCATCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  2:4092018/101‑6 (MQ=12)                                        CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  1:2421261/101‑6 (MQ=32)                                        CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  1:2605135/101‑6 (MQ=32)                                        CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                         <  1:1473706/101‑6 (MQ=32)                                          CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                       >  2:1636330/1‑101 (MQ=32)                                          CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                       <  2:524832/101‑1 (MQ=32)                                          CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                       <  1:4038548/101‑1 (MQ=32)                                           AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTG                                                                      <  1:2539571/101‑1 (MQ=32)                                           AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACCCCCGCACCCCCGTGGGGTATTTG                                                                      >  2:1549445/1‑101 (MQ=0)                                            GCACCGCGACGCGCGCTCCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGa                                                                     <  1:2640741/101‑2 (MQ=18)                                            GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGa                                                                     >  1:2613461/1‑100 (MQ=33)                                            GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGa                                                                     <  1:3757276/101‑2 (MQ=33)                                            GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGa                                                                     <  1:2696244/101‑2 (MQ=33)                                            GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGa                                                                     >  1:549673/1‑100 (MQ=33)                                             CACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCCTGGGATATTTGag                                                                    >  1:1467217/1‑99 (MQ=21)                                              ACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGagg                                                                   <  2:2777043/101‑4 (MQ=35)                                               CCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGaggc                                                                  <  1:3735908/101‑5 (MQ=37)                                                CGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTGaggca                                                                 >  2:2446245/1‑96 (MQ=38)                                                                                                                                                                                                                     CGCAATGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT...................................................................................................  <  NC_014034/1608162‑1608051 ....................................................................................................AGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTGCGCCAAGAAAAAGCACAGACTTTTGCCCGTTCACCCTGGCGCAAATCTCCCGGGGGGAGAGTGGCGCA  >  NC_014034/2808467‑2808565 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG