New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	16 (0.070)	36 (0.160)	5/186	25.8	0.23	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	3504133 =	228 (0.930)					intergenic (‑26/+57)	recO/RCAP_rcc03309	DNA repair protein RecO/hypothetical protein
Rejected: Position hash score below cutoff.

TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ....................................................................................................CGGGGGTTTTGCACCCCCGGGCCCCCGCAGGATATTTGAGGCAAGATAAAAGCGAAAGCCGGGGTCAGTCTTTCAGTCCGTCTTCATCCAGAAGCGTGCGGCCGTGC  >  NC_014034/3504133‑3504232                                                                                                                                                                                                                        GCCGTGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     <  1:3309815/101‑1 (MQ=1)        GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     <  1:3578087/101‑1 (MQ=1)        GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     >  2:4609697/1‑101 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    >  2:1646208/1‑101 (MQ=1)         CCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTT                                                                                                    <  1:2219632/101‑1 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  2:4450889/101‑2 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  1:2856562/101‑2 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   >  2:2526301/1‑100 (MQ=1)           ggGGCCAGCCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:4537826/99‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCGCCAGCACCGCTACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:2850056/101‑3 (MQ=0)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcc                                                                                                  >  2:1335094/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  1:1579751/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  1:4143501/101‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  2:1501202/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  2:4665313/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTca                                                                                                  >  1:3201730/1‑99 (MQ=1)           GTGGCCAGACCCGAGCCCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:2076785/101‑3 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 <  1:2998735/101‑4 (MQ=1)            TGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCAAATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcac                                                                                                 <  2:1904457/101‑4 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcaca                                                                                                >  2:367163/1‑97 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTcacc                                                                                                >  1:1809007/1‑97 (MQ=1)             GGCCAGACCCGAGCCCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcaca                                                                                                <  1:1054509/101‑5 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               <  1:367216/101‑6 (MQ=1)               CCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACC                                                                                              >  2:895569/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             <  2:3464337/101‑1 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             <  2:4952171/101‑1 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTCACACCCC                                                                                            >  1:2017464/1‑101 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  1:819010/101‑1 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  1:236446/101‑1 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           <  2:579039/101‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  2:1199122/101‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  2:228640/101‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGGTTTCCCCCCCCc                                                                                          >  1:167783/1‑100 (MQ=255)                    CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGc                                                                                         <  2:1089811/101‑2 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcac                                                                                       <  1:946472/101‑4 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      <  2:3897873/101‑5 (MQ=1)                                                                                                                                                                                                                 TGCCGCCGCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGT....................................................................................................  <  NC_014034/1608157‑1608051 ....................................................................................................CGGGGGTTTTGCACCCCCGGGCCCCCGCAGGATATTTGAGGCAAGATAAAAGCGAAAGCCGGGGTCAGTCTTTCAGTCCGTCTTCATCCAGAAGCGTGCGGCCGTGC  >  NC_014034/3504133‑3504232 Base quality scores:  ATCG  < 3 ≤  ATCG  < 20 ≤  ATCG  < 29 ≤  ATCG  < 34 ≤  ATCG  < 40 ≤  ATCG