New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	3735261 =	15 (0.870)	6 (0.380)	4/278	NT	26.8%	coding (632/849 nt)	yiaJ	transcriptional repressor of yiaK‑S operon
	?	CP009273	3735587 =	19 (1.200)					coding (306/849 nt)	yiaJ	transcriptional repressor of yiaK‑S operon

AAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAA  >  CP009273/3735039‑3735503                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                   aaGCGTTATGTGATCGCGCCCATGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTTGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAg                                                                                                                                                                                                <  1:59049/275‑1 (MQ=255)                                                                                           agaTTTTTCTCTCCCACCTGATTGAGCCGGGATGTCGAAAGCGAAATCGAGACGGCGTACGGCACCCGCCCATGAATATGAAACACCGGAACAGCAATAGAGGAGACGCCGAGTTCATTTTCTTCTCTGTCCATCGCCGCTCCGCTTTGCCGAGTGTGCTCCAGGTCGTGGAACATCGCGGGCCGCTAGGTACTGGAATTGAGGGTTAAGGGCTGGCTCTCATGCAGGTGGCTTTCACCGTATGACGTACCGTCGTCGGGGGGACGaaatgaaat                                                                                                      >  2:43488/1‑269 (MQ=255)                                                                                                                     aCGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACCCCGGAACCGCAATCCCGTATCCTCCTCTTTCTTTTTCTTCTGTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTACTGGTATTGCGTGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCAGTGCTTGCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGt                                                                            >  1:184665/1‑275 (MQ=255)                                                                                                                        ttatttCGAAAGCGAATTCGACACGGCTTACGGCACCCGTCCATTAATATCAAACACCGGAACAGCAATACAGGTGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTGTCACGAATGTGCGACAGTTCGTCGAACATCGCGGGCAGCACGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTaga                                                                         <  1:43489/270‑1 (MQ=255)                                                                                                                                                                  cctgaccaccaaatttattgccgtcgggcagaaggcgctgtcttcgctgaatatcattcatATCGCCGCTCCGCTTTCACGAATGTgc                                                                                                                                                                                                                          <  1:136948‑M1/27‑1 (MQ=255)                                                                                                                                                                  cctgaccaccaaatttattgccgtcgggcagaaggcgctgtcttcgctgaatatcattcatATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCGGGTTAAc                                                                                                                                                                       <  2:123505‑M1/78‑1 (MQ=255)                                                                                                                                                                  cctgaccaccaaatttattgccgtcgggcagaaggcgctgtcttcgcggaatatcattcatATCGCCGCTCCGCTTTCCCGCATGTGCGCCAGTTCGTCGAAGATCGCGGCCAGCGCGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCAAGTATGACTTCACGTATTCCGGGTGACCAAACGCCATGTAGATGTTGCCCAtt                                                                                      <  1:324025‑M1/159‑1 (MQ=255)                                                                                                                                                                      accaccaaatttattgccgtcgggcagaaggcgctgtcttcgctgaatatcattcatATCGCCGCTCCGCTTTCACGAATGTGCGCCa                                                                                                                                                                                                                      >  2:136946‑M1/58‑88 (MQ=255)                                                                                                                                                                      accaccaaatttattgccgtcgggcagaaggcgctgtcttcgctgaatatcattcatATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCGGGTTAACGGCt                                                                                                                                                                   >  1:123507‑M1/58‑139 (MQ=255)                                                                                                                                                                                 cgaaaCAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTTCGCCAGTTCGTCTAACATCGCGGGCAGCCCGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCCCGTAGTCCGGGTGACCAAACGCCATGTCGATCTTGCCCATTGCGTAACAGTAGAGCGGCATATGCTGGCCAAAATAGGCACGGGTTCACCGCATCCCGGAtggcgtgcaca                >  2:45182/4‑266 (MQ=255)                                                                                                                                                                                 cGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGccgctccgct                                                                                                                                                                                                                                       >  1:44106/1‑60 (MQ=255)                                                                                                                                                                                   gAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCgg                                                                                                                                                                                                    >  1:168401/1‑93 (MQ=255)                                                                                                                                                                                   gAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCg                                                                                                                                                                              >  1:184131/1‑115 (MQ=255)                                                                                                                                                                                     aCAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCa                                                                                                                                                                                                                                   <  2:44105/60‑1 (MQ=255)                                                                                                                                                                                       aGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAg                                                                                                                                                                                                <  2:168397/93‑1 (MQ=255)                                                                                                                                                                                       aGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCGGGtt                                                                                                                                                                          <  2:184127/115‑1 (MQ=255)                                                                                                                                                                                               aGGGGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCaaa  <  1:45183/275‑1 (MQ=255)                                                                                                                                                                                                      gCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGt                                                                                                                                                                                    >  1:80297/1‑90 (MQ=255)                                                                                                                                                                                                          aGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGGAGCTCGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCaa                                                                                                             <  1:108454/157‑1 (MQ=255)                                                                                                                                                                                                          aGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTg                                                                                                                                                                                <  2:80295/90‑1 (MQ=255)                                                                                                                                                                                                                        cattcatATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCgg                                                                                  >  1:135052‑M1/8‑170 (MQ=255)                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                   AAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGCCGCTCCGCTTTCACGAATGTGCGCCAGTTCGTCGAACATCGCGGGCAGCTCGGTAATGGTATTGCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAA  >  CP009273/3735039‑3735503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ 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.