New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3741900 =	164 (1.450)	4 (0.040)	3/412	NT	2.8%	coding (632/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon
	?	NC_000913	3742226 =	120 (1.130)					coding (306/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon

TATTTTGATTTATAAGCTGGAACCCACAACCGGGATGCTGCGAACCCGTGCCTATATTGGCCAGCATATGCCGCTCTACTGTTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3742145‑3741900 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcggagcggcgatATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACGGTACTCTTATTTAAACCAGCCAGCTCCGAAAGATGCGCCAACGGACAACCGTTTGGATAGTTGCTCAAAATCTCAATCAGCATCAACCCGCGAAACAG  >  NC_000913/3742226‑3742456                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TATTTTGATTTATAAGCTGGAACCCACAACCGGGATGCTGCGAACCCGTGCCTATATTGGCCAGCATATGCCGCTCTACTGTTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGA                                                                                                                                                                                                                                                 >  1:590733/1‑238   TTTTGATTTATAAGCTGGAACCCACAACCGGGATGCTGCGAACCCGTGCCTATATTGGCCAGCATATGCCGCTCTACTGTTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCG                                                                                                                                                                                                                                              >  2:680631/1‑239      ttattttaaggcttgtaccaaaAACCGGGATGCTGCGATCCAGTGCCTATATTGGCCAGCATATGCCTCTCTACTGTTACTCAATAGGCAAGATCTACATGGCGTTTAGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCTGAGCGGCG                                                                                                                                                                                                                                           <  1:201032/217‑1      TGATTTATAAGCTGGAACCCACAACCGGGATGCTGCGAACCCGTGCCTATATTGGCCAGCATATGCCGCTCTACTGTTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCG                                                                                                                                                                                                                                           <  1:101141/239‑1      TGATTTATAAGCTGGAACCCACAACCGGGATGCTGCGAACCCGTGCCTATATTGGCCAGCATATGCCGCTCTACTGTTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCG                                                                                                                                                                                                                                           <  1:887153/239‑1      TGATTTATAAGCTGGAACCCACAACCGGGATGCTGCGAACCCGTGCCTATATTGGCCAGCATATGCCGCTCTACTGTTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCG                                                                                                                                                                                                                                           <  2:988358/239‑1                                                                     TGCCGCTCTACTGTTCCTCAATGGGCAAGACCTACATGGCGTTTGGTCGCCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGG                                                                                                                                                                            <  2:832513/239‑1                                                                                  TTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAG                                                                                                                                                                                                                                                <  1:415158/158‑1                                                                                  TTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAG                                                                                                                                                                                                                                                >  2:415158/1‑158                                                                                               AAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGT                                                                                                                                                  <  2:355983/239‑1                                                                                                             GTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGG                                                                                                                                                                            >  1:1160539/1‑199                                                                                                             GTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGG                                                                                                                                                                            <  2:1160539/199‑1                                                                                                                                                                                                                                           CGGAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACGGTACTCTTATTTAAACCAGCCAGCTCCGAAAGATGCGCCAACGGACAACCGTTTGGATAGTTGCTCAAAATCTCAATCAGCATCAACCCGCGAA      >  2:352417/1‑239                                                                                                                                                                                                                                             GAGCGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACGGTACTCTTATTTAAACCAGCCAGCTCCGAAAGATGCGCCAACGGACAACCGTTTGGATAGTTGCTCAAAATCTCAATCAGCCTCAACCCGCGACAC    >  1:581792/1‑239                                                                                                                                                                                                                                                CGGCGATATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACGGTACTCTTATTTAAACCAGCCAGCTCCGAAAGATGCGCCAACGGACAACCGTTTGGATAGTTGCTCAAAATCTCAATCAGCATCGACCCGCGAAACAG  >  2:64523/1‑238                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TATTTTGATTTATAAGCTGGAACCCACAACCGGGATGCTGCGAACCCGTGCCTATATTGGCCAGCATATGCCGCTCTACTGTTCCGCAATGGGCAAGATCTACATGGCGTTTGGTCACCCGGACTACGTGAAGTCATACTGGGAAAGCCATCAGCATGAGATCCAGCCGTTAACCCGCAATACCATTACCGAGCTGCCCGCGATGTTCGACGAACTGGCGCACATTCGTGAAAGCGGAGCGGCGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3742145‑3741900 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gcggagcggcgatATGAATGATATTCAGCGAAGACAGCGCCTTCTGCCCGACGGCAATAAATTTGGTGGTCAGGCGATAACTCCCTGCGGCAGGCGCGGTGGTCACATAGCCGCAGGACTGTAATCCCTGCAATAAGCGATGGACGGTACTCTTATTTAAACCAGCCAGCTCCGAAAGATGCGCCAACGGACAACCGTTTGGATAGTTGCTCAAAATCTCAATCAGCATCAACCCGCGAAACAG  >  NC_000913/3742226‑3742456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ 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.