New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_014034	1608051 =	7 (0.030)	34 (0.150)	4/186	34.9	0.25	intergenic (+321/‑26)	RCAP_rcc01484/murD	hypothetical protein/UDP‑N‑acetylmuramoylalanine‑‑D‑glutamate ligase
	?	NC_014034	3504133 =	199 (0.840)					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                                                                                                                                                                                                                        GCCGTGGCCAGACCCGAGCGCCCGATCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     <  2:727648/101‑1 (MQ=1)        GCCGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTT                                                                                                     >  1:3867113/1‑101 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  2:3866828/101‑2 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTc                                                                                                   <  2:3356485/101‑2 (MQ=1)          CGTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAACTGCGGGGGTTgc                                                                                                   >  2:834355/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATCTCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGCGGTTcca                                                                                                  >  2:4389953/1‑98 (MQ=0)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  2:4602531/101‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  <  1:645147/101‑3 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  1:1525172/1‑99 (MQ=1)           GTGGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTca                                                                                                  >  1:2720724/1‑99 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcaca                                                                                                <  1:168321/101‑5 (MQ=1)             GGCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcaca                                                                                                >  1:3640183/1‑97 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               >  2:4478065/1‑96 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               <  1:226250/101‑6 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               >  2:2902325/1‑96 (MQ=1)              GCCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTcacac                                                                                               >  2:2725233/1‑96 (MQ=1)               CCAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACC                                                                                              >  1:4424186/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             >  1:175157/1‑101 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             <  2:1996607/101‑1 (MQ=1)                CAGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCC                                                                                             >  2:4399020/1‑101 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                            <  1:3173785/101‑1 (MQ=1)                 AGACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCC                                                                                            >  2:3921231/1‑101 (MQ=1)                  GACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCC                                                                                           >  1:2888433/1‑101 (MQ=1)                   cCCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  1:1899089/100‑1 (MQ=1)                   ACCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCG                                                                                          <  1:1758146/101‑1 (MQ=1)                    CCCGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGc                                                                                         <  2:4423894/101‑2 (MQ=1)                    CCCGAGCCCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGc                                                                                         <  2:548541/101‑2 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcac                                                                                       <  1:4122887/101‑4 (MQ=1)                      CGAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcac                                                                                       <  2:1863904/101‑4 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      >  2:1235654/1‑97 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      <  2:704335/101‑5 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      <  1:3406527/101‑5 (MQ=1)                       GAGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcacc                                                                                      <  2:1525063/101‑5 (MQ=1)                        AGCGCCCGAGCCCCAGCACCGCGACGCGCGCACCCTCATATCCCTGAACCGGTATCATCTGCGACCTCCGTAAGCTGCGGGGGTTTCACACCCCCGcaccc                                                                                     >  2:4384047/1‑96 (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