New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	0 (0.000)	53 (0.270)	24/184	16.6	0.40	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	= 1820392	161 (0.760)					intergenic (+83/‑103)	RCAP_rcc01683/RCAP_rcc01684	terminase‑like family protein/HK97 family phage portal protein
Rejected: Position hash score below cutoff.

ATGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608158‑1608051 ....................................................................................................GCGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTTCACCAAGAAAAAACACGCAGCTTTTTCCTGGTCCAAATACGCCCTTGCGCGCTCAAAGCCCGCGCACCT  <  NC_014034/1820392‑1820293                                                                                                                                                                                                                          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                                                                                         <  2:4196751/101‑1 (MQ=1)                     CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGC                                                                                         <  1:1762847/101‑1 (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                                                                          <  1:1473706/101‑6 (MQ=32)                                    CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  1:2421261/101‑6 (MQ=32)                                    CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  1:2605135/101‑6 (MQ=32)                                      CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                        >  2:1636330/1‑101 (MQ=32)                                      CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                        <  1:4038548/101‑1 (MQ=32)                                      CAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTT                                                                        <  2:524832/101‑1 (MQ=32)                                       AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTg                                                                       <  1:2539571/101‑2 (MQ=32)                                       AGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACCCCCGCACCCCCGTGGGGTATTTg                                                                       >  2:1549445/1‑100 (MQ=0)                                        GCACCGCGACGCGCGCTCCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTga                                                                      <  1:2640741/101‑3 (MQ=18)                                        GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTga                                                                      >  1:2613461/1‑99 (MQ=33)                                        GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTga                                                                      <  1:2696244/101‑3 (MQ=33)                                        GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTga                                                                      >  1:549673/1‑99 (MQ=33)                                        GCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTga                                                                      <  1:3757276/101‑3 (MQ=33)                                          ACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgagg                                                                    <  2:2777043/101‑5 (MQ=35)                                           CCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgaggc                                                                   <  1:3735908/101‑6 (MQ=37)                                                                                                                                                                                                                  ATGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608158‑1608051 ....................................................................................................GCGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTTCACCAAGAAAAAACACGCAGCTTTTTCCTGGTCCAAATACGCCCTTGCGCGCTCAAAGCCCGCGCACCT  <  NC_014034/1820392‑1820293 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 33 ≤  ATCG  < 39 ≤  ATCG