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

GCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACGG  >  CP009273/3735329‑3735720                                                                                                                                                                                                                                                                   |                                                                                                                                      gCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGAGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGACTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGTAGCGGCGATATGAATGATATTAAGCg                                                                                                                       >  1:321353/1‑275 (MQ=255)                                    cccAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTtg                                                                                    >  1:96642/1‑275 (MQ=255)                                         tATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATatgaatg                                                                                                                                 >  2:196219/1‑225 (MQ=255)                                             aCTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGatat                                                                                                                             <  1:196223/225‑1 (MQ=255)                                                       gTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTACAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAAAAGTTAATGTTTTCACCAGTGGCGATGTTACGTGCCTCAAGCTGCGGAGCGGCGATATTAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGATGGTCAGGCGATAACTcc                                                                 >  1:171628/1‑275 (MQ=255)                                                        tCCGGGAGACCAAACGACATGTAGATCTTGCCCATTGCGGAACAATAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCNCAAGATGCGGAGCGGCGATatgaatg                                                                                                                                 >  1:244823/1‑210 (MQ=255)                                                            ggTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGatat                                                                                                                             <  2:244815/210‑1 (MQ=255)                                                                                                ccgcaatgggcaagatctacatggcgtttggtcacccggactacgtgaagtcatactgggaaagccatcagcatgagatccagccgttaacccgcaataccattaccgagctgcccgcgatgttcgacgaactggcgcacattcgtgaaagcggagcggcgatatgaatg                                                                                                                                 >  1:135052‑M2/164‑170 (MQ=255)                                                                                                    aatgggcaacatctacatggcgtttggtcacccggaatacgtgaagtcatacttggaaagccatcagcatgagatccagccgttaacccgcaataccattaccgcgctggccgcgatcttcgacgaactggcgcacatgcgggaaagcggagcggcgatATGAATGATATTCCGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAgg                                                                           <  1:324025‑M2/61‑1 (MQ=255)                                                                                                             cATATGCTGGCCAAGATAGGCACGGGTTCGCAGCATCCCGGTTGGGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGNCCGACGGCCATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGCCTGCAATCCCAGCAATacac           >  1:252293/1‑272 (MQ=255)                                                                                                               tatGCTGGCCAATATAGGCACGGGTTCGCAGCCTCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGACGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTACCTGCGGCAGGCGCGGTGGACACATAGc                                      >  1:141755/1‑246 (MQ=255)                                                                                                                    tGGCCAATATAGGCACGGGTTCGCAGCATCCCCGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGa     >  1:54542/1‑274 (MQ=255)                                                                                                                      gCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATa                                        >  1:196211/1‑237 (MQ=255)                                                                                                                       tgtaaatcggCATGGGTTGGGAGCCTACCGGTTTTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACgg  <  2:96640/266‑1 (MQ=255)                                                                                                                          atatAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCg                                    <  2:196207/237‑1 (MQ=255)                                                                                                                           tataGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATatgaatg                                                                                                                                 >  2:321775/1‑143 (MQ=255)                                                                                                                               ggCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGatat                                                                                                                             <  1:321787/143‑1 (MQ=255)                                                                                                                                gCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGc                                                                                                                        >  2:56744/1‑147 (MQ=255)                                                                                                                                    gggTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAg                                                                                                                    <  1:56746/147‑1 (MQ=255)                                                                                                                                                                                 agccgttaacccgcaataccattaccgagctgcccgcgatgttcgacgaactggcgcacattcgtgaaagcggagcggcgatATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTggtggt                                                                               >  1:123507‑M2/83‑139 (MQ=255)                                                                                                                                                                                    cGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGc                                                                                                      >  1:154600/1‑113 (MQ=255)                                                                                                                                                                                     gttaacccgcaataccattaccgagctgcccgcgatgttcgacgaactggcgcacattcgtgaaagcggagcggcgatATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAgg                                                                           <  2:123505‑M2/61‑1 (MQ=255)                                                                                                                                                                                        aTCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGa                                                                                                  <  2:154596/113‑1 (MQ=255)                                                                                                                                                                                                                                    tggcgcacattcgtgaaagcggagcggcgatATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTggtggt                                                                               >  2:136946‑M2/32‑88 (MQ=255)                                                                                                                                                                                                                                        gcacattcgtgaaagcggagcggcgatATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAgg                                                                           <  1:136948‑M2/61‑1 (MQ=255)                                                                                                                                                                                                                                                                   |                                                                                                                                      GCGGGTTAACGGCTGGATCTCATGCTGATGGCTTTCCCAGTATGACTTCACGTAGTCCGGGTGACCAAACGCCATGTAGATCTTGCCCATTGCGGAACAGTAGAGCGGCATATGCTGGCCAATATAGGCACGGGTTCGCAGCATCCCGGTTGTGGGTTCCAGCTTATAAATCAAAATAGCGTGATCGTCTTCGCGGCTGGAGAAGTTAATGGTTTCACCAGTGGCGATGTTCAGTGCCTCAAGATGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACGG  >  CP009273/3735329‑3735720

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 36 ≤ 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.