New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	23 (0.100)	47 (0.200)	3/200	31.4	0.27	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	3407065 =	233 (0.980)					intergenic (+21/‑184)	ileS/RCAP_rcc03205	isoleucyl‑tRNA synthetase/hypothetical protein
Rejected: Position hash score below cutoff.

GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT............................................  <  NC_014034/1608150‑1608051 ....................................................................................................TTCGCGCCCCCGGACCCCCGCGGGATATTTGAGGCAAGATGAAA  >  NC_014034/3407065‑3407108                                                                                                                                                  GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                             >  2:4119528/1‑101 (MQ=1)  CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                            <  1:1329276/101‑1 (MQ=1)  CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                            <  2:383829/101‑1 (MQ=1)  CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                            <  2:2912059/101‑1 (MQ=1)   CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTC                                           >  1:3160918/1‑101 (MQ=1)    GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCa                                          >  1:4590577/1‑100 (MQ=1)    GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCa                                          >  2:3105157/1‑100 (MQ=1)     ggcCCACACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCac                                         <  2:1190334/98‑3 (MQ=0)     TGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCac                                         <  2:2394474/101‑3 (MQ=1)     TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCac                                         <  1:1157226/101‑3 (MQ=1)      GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCaca                                        <  1:3929269/101‑4 (MQ=1)       GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCacac                                       <  2:2946285/101‑5 (MQ=1)       GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCacac                                       >  2:364046/1‑97 (MQ=1)       GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCacac                                       <  2:855903/101‑5 (MQ=1)        CCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCacacc                                      <  2:3026349/101‑6 (MQ=1)         CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                     >  2:4448792/1‑101 (MQ=1)         CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                     >  1:4524037/1‑101 (MQ=1)         CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                     >  1:645806/1‑101 (MQ=1)          AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                    >  2:1349137/1‑101 (MQ=1)          AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                    <  2:536855/101‑1 (MQ=1)          AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                    >  1:4734365/1‑101 (MQ=1)           GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                   <  1:1055869/101‑1 (MQ=1)           GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                   >  2:1537257/1‑101 (MQ=1)           GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                   >  2:2115093/1‑101 (MQ=1)           GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                   <  1:325752/101‑1 (MQ=1)            ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCc                                  >  2:1612293/1‑100 (MQ=11)            ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                  <  2:118498/101‑1 (MQ=1)            ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                  <  2:2379132/101‑1 (MQ=1)              CCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcc                                >  1:2972629/1‑99 (MQ=1)               CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCCCACCCCCGcat                               <  2:1752805/101‑4 (MQ=1)               CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCAC                               <  2:475688/101‑1 (MQ=1)               CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCAC                               <  1:2902652/101‑1 (MQ=1)                GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACC                              >  2:4712891/1‑101 (MQ=1)                GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACC                              <  1:2058585/101‑1 (MQ=1)                GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACC                              <  2:3998167/101‑1 (MQ=1)                GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACC                              <  2:2498626/101‑1 (MQ=1)                GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACC                              <  1:716329/101‑1 (MQ=1)                  GCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCC                            <  1:2922056/101‑1 (MQ=1)                  GCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCC                            >  1:3035515/1‑101 (MQ=1)                  GCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCC                            <  1:3519651/101‑1 (MQ=1)                   CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCC                           <  2:410800/101‑1 (MQ=1)                   CGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCC                           <  1:1335577/101‑1 (MQ=1)                    GCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCG                          >  1:4426929/1‑101 (MQ=1)                     CCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGt                         <  2:649738/101‑2 (MQ=1)                      CCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGtg                        >  1:181324/1‑99 (MQ=1)                      CCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGCACCCCCGtg                        <  1:4182095/101‑3 (MQ=1)                                            GCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACGCCCCCGCACCCCCGTGGGATATTTGAGGCAAGATGAAA  <  2:3552493/101‑1 (MQ=12)                                                                                                                                                  GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT............................................  <  NC_014034/1608150‑1608051 ....................................................................................................TTCGCGCCCCCGGACCCCCGCGGGATATTTGAGGCAAGATGAAA  >  NC_014034/3407065‑3407108 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 28 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG