New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	2343937 =	35 (0.710)	4 (0.090)	4/238	NT	12.4%	coding (412/456 nt)	soxR	DNA‑binding transcriptional regulator
	?	NC_002947	2343971 =	23 (0.490)					coding (378/456 nt)	soxR	DNA‑binding transcriptional regulator

AGCGACTGTTTGTCACCTGCAGGTCATGCGCGCCGGCATAGATTCGCATCTGACATGAGCGTGCTAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACATCTCGCTCCATTGTGCGGCCGTGAGCTTGCTGTTGGGG  >  NC_002947/2343825‑2344115                                                                                                                                                    |                                                                                                                                                 cgagatgtccacggcctggcgcgaagacctgaatgcccgcattcgcacactggaagcactgcgcgacagcctcgacaactgcattggctgcggttgcctgtcgctggaggacTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGtcc                                                                                                                                               >  2:868646‑M1/113‑150 (MQ=255)          cacggcctggcgcgaagacctgaatgcccgcattcgcacactggaagcactgcgcgacagcctcgacaactgcattggctgcggttgcctgtcgctggaggacTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAg                                                                                                                                                  <  2:1108059‑M1/35‑1 (MQ=255)          cacggcctggcgcgaagacctgaatgcccgcattcgcacactggaagcactgcgcgacagcctcgacaactgcattggctgcggttgcctgtcgctggaggacTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAg                                                                                                                                                  >  1:1108059‑M1/104‑138 (MQ=255)                                       tAGATTCGCATCTGACATGAGCGTGCTAGGTTAGCCTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCTCATCCT‑GGCGTAGTTGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAGTGCGGTTGGCGAg                                                                                                         <  2:685502/150‑1 (MQ=255)                                         gATTCGCATCTGACATGAGCGTGCTAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTCGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGc                                                                                                       <  1:236348/150‑1 (MQ=255)                                           ttCGCATCTGACATGAGCGTGCTAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTg                                                                                                     >  2:1063581/1‑150 (MQ=255)                                           ttCGCATCTGACATGAGCGTGCTAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTg                                                                                                     >  1:376855/1‑150 (MQ=255)                                             ctcATCTGACATGAGCGTGCTAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTc                                                                                                   <  1:143239/148‑1 (MQ=255)                                                             gTGCTAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAgt                                                                                   <  1:1015421/150‑1 (MQ=255)                                                                 tAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCtt                                                                                        >  1:185452/1‑141 (MQ=255)                                                                 tAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCtt                                                                                        <  2:185452/141‑1 (MQ=255)                                                                       aGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGtt                                                                                                               >  2:837715/1‑112 (MQ=255)                                                                       aGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGtt                                                                                                               <  1:837715/112‑1 (MQ=255)                                                                              cttcttTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAgg                                                                                                                                   >  1:423250/1‑85 (MQ=255)                                                                              cttcttTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAgg                                                                                                                                   <  2:423250/85‑1 (MQ=255)                                                                               ttcttTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGtc                                                                                                                                                >  1:287718/1‑71 (MQ=255)                                                                               ttcttTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGtc                                                                                                                                                <  2:287718/71‑1 (MQ=255)                                                                               ttcttTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTc                                                                 >  2:820372/1‑150 (MQ=255)                                                                                       gAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCATCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTc                                                         >  1:169573/1‑150 (MQ=255)                                                                                              cgcgCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCa                                                                                              <  1:486900/106‑1 (MQ=255)                                                                                              cgcgCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCa                                                                                              >  2:486900/1‑106 (MQ=255)                                                                                               gcgcCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGTATTTGGGCATTCAGGTCTTCGCGCCAgg                                                 >  1:643382/1‑150 (MQ=255)                                                                                               gcgcCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAgg                                                 >  1:1100040/1‑150 (MQ=255)                                                                                                   cccGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGt                                             <  1:1213919/150‑1 (MQ=255)                                                                                                        tCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACa                                        <  1:105441/150‑1 (MQ=255)                                                                                                          ccttccttGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGc                                                                         <  2:117240/115‑1 (MQ=255)                                                                                                          ccttccttGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGc                                                                         >  1:117240/1‑115 (MQ=255)                                                                                                              ggactgcccactgcgcaaccccgaggatgtgctgggcaGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACATCTCg                                   >  2:868646‑M2/39‑150 (MQ=255)                                                                                                                 ctgcccactgcgcaaccccgaggatgtgctgggcaGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTg                                            <  2:1108059‑M2/103‑1 (MQ=255)                                                                                                                 ctgcccactgcgcaaccccgaggatgtgctgggcaGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTg                                            >  1:1108059‑M2/36‑138 (MQ=255)                                                                                                                        cacaTCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACATCTCGCTCCATTGTGc                        <  1:1063581/150‑1 (MQ=255)                                                                                                                         tgcgcaaccccgaggatgtgctgggcaGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACATCTCGCTCCATTGTGc                        <  1:868646‑M2/123‑1 (MQ=255)                                                                                                                                          gcAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACATCTCGCTCCATTGTGCGGCCGTGAGCTTGCTGt       >  1:132741/1‑150 (MQ=255)                                                                                                                                               gggcaGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACATCTCGCTCCATTGTGCGGCCGTGAGCTTGCTGTTgggg  <  1:820372‑M2/145‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                 AGCGACTGTTTGTCACCTGCAGGTCATGCGCGCCGGCATAGATTCGCATCTGACATGAGCGTGCTAGGTTAGCGTGCCTTCTTTTCGAGGATCCGCGCCCCGGTCCCTTCCTTGCCCAGCACATCCTCGGGGTTG‑CGCAGTGGGCAGTCCTCCAGCGACAGGCAACCGCAGCCAATGCAGTTGTCGAGGCTGTCGCGCAGTGCTTCCAGTGTGCGAATGCGGGCATTCAGGTCTTCGCGCCAGGCCGTGGACATCTCGCTCCATTGTGCGGCCGTGAGCTTGCTGTTGGGG  >  NC_002947/2343825‑2344115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.