New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	0 (0.000)	49 (0.240)	22/184	19.8	0.37	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	= 1820392	169 (0.750)					intergenic (+83/‑103)	RCAP_rcc01683/RCAP_rcc01684	terminase‑like family protein/HK97 family phage portal protein
Rejected: Position hash score below cutoff.

TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ...................................................................................................GCGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTTCACCAAGAAAAAACACGCAGCTTTTTCCTGGTCCAAATACGCCCTTGCGCGCTCAAAGCCCGCGCACCT  <  NC_014034/1820392‑1820293                                                                                                                                                                                                                        GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     >  1:4366978/1‑101 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    <  2:2170299/101‑1 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTC                                                                                                   >  1:2921619/1‑101 (MQ=1)           GTGGCCAGACCCGAGCGCCAGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCA                                                                                                  <  1:2527691/101‑1 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACA                                                                                                <  1:2152608/101‑1 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACA                                                                                                <  1:3113801/101‑1 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACA                                                                                                <  1:980875/101‑1 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACc                                                                                                >  1:3956094/1‑100 (MQ=1)                cggcCCCGAGCGCCGGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             <  2:1716454/97‑1 (MQ=0)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             >  2:3197532/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             <  2:3049709/101‑1 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             >  2:2855529/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCTCACCC                                                                                             >  1:3818337/1‑101 (MQ=0)                  gcCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  2:1623668/99‑1 (MQ=1)                   cCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  1:4362308/100‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  2:2848497/101‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          >  2:869692/1‑101 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  1:2337936/101‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACCCCCc                                                                                          >  1:397238/1‑100 (MQ=11)                    CCCGAGCGCCCGATCCCCAGCACCGCGACGCGCGTACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGC                                                                                         <  1:3828054/101‑1 (MQ=0)                    CCCGAGCGCCCGAGCCCCAGCAGCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGC                                                                                         <  2:755784/101‑1 (MQ=1)                    CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACCCCCGC                                                                                         >  2:3919940/1‑101 (MQ=1)                     CCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCA                                                                                        >  1:1709026/1‑101 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACC                                                                                      <  1:515676/101‑1 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGAACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACC                                                                                      >  2:1703473/1‑101 (MQ=1)                        AGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCC                                                                                     <  1:2050041/101‑1 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCC                                                                                   <  2:1908984/101‑1 (MQ=1)                          CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCC                                                                                   <  2:329141/101‑1 (MQ=1)                           gatcgcGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCG                                                                                  >  2:2336477/7‑101 (MQ=0)                           GCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCG                                                                                  <  2:3170388/101‑1 (MQ=1)                            CCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGT                                                                                 >  2:3118282/1‑101 (MQ=1)                              CGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGG                                                                               >  2:1535502/1‑101 (MQ=1)                              CGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGG                                                                               <  1:2650944/101‑1 (MQ=1)                              CGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGG                                                                               <  2:4439006/101‑1 (MQ=1)                               catCCCCTGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGg                                                                              >  2:2250326/4‑100 (MQ=2)                                AGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGCGGga                                                                             >  1:3544309/1‑99 (MQ=14)                                 GCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgat                                                                            <  2:3955838/101‑4 (MQ=32)                                 GCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgat                                                                            <  2:3630334/101‑4 (MQ=32)                                 GCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgat                                                                            <  1:3574344/101‑4 (MQ=32)                                  CCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgata                                                                           <  1:3295529/101‑5 (MQ=32)                                   CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  2:1502492/101‑6 (MQ=32)                                   CCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGgatat                                                                          <  1:3687742/101‑6 (MQ=32)                                    CCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATT                                                                         <  1:1741914/101‑1 (MQ=32)                                    CCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATT                                                                         >  1:2587108/1‑101 (MQ=32)                                    CCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATT                                                                         <  1:3468806/101‑1 (MQ=32)                                        CACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgag                                                                     >  1:2155043/1‑98 (MQ=34)                                        CACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgag                                                                     <  2:3366918/101‑4 (MQ=34)                                        CACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgag                                                                     <  1:1674548/101‑4 (MQ=34)                                         ACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGTGGGATATTTgagg                                                                    <  2:2118075/101‑5 (MQ=35)                                                                                                                                                                                                                 TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ...................................................................................................GCGGGGGTTTCACACCCCCGCACCCCCGTGGCGTATTTTCACCAAGAAAAAACACGCAGCTTTTTCCTGGTCCAAATACGCCCTTGCGCGCTCAAAGCCCGCGCACCT  <  NC_014034/1820392‑1820293 Base quality scores:  ATCG  < 3 ≤  ATCG  < 21 ≤  ATCG  < 30 ≤  ATCG  < 34 ≤  ATCG  < 39 ≤  ATCG