New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2407180 =	0 (0.000)	34 (1.120)	32/484	0.1	100%	intergenic (‑539/‑381)	lrhA/alaA	DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA
	?	NC_000913	3583428 =	NA (NA)					noncoding (1/768 nt)	IS1	repeat region

ATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCG  >  NC_000913/3583189‑3583672                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                     aTGAAGTTAGTATTCTTCTTCAGAATCAACCTCATTATATTCATTTTTTAAGCGCAATGGATGGCTTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAACAACCTTTTTGCCGTACATGAATTTTATCGAAATAATGATGATTTCATACACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATCTTTACTTATGACATTAAAGGTGATGCTGcc                                                                                                                                                                                                                                           >  2:280779/1‑251 (MQ=255)                     aagaagCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCGCGAGTCCAGAACCTTCAGGTAAAAACCTTTTTGCCGTAAATGAATGTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGTTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTat                                                                                                                                                                                                                       <  2:8873/251‑1 (MQ=255)                     aaGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTat                                                                                                                                                                                                                       <  2:8881/251‑1 (MQ=255)                      aGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGCTTCAAGCAACTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTCCAAGAACGGTTCGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTatg                                                                                                                                                                                                                      >  1:294116/1‑251 (MQ=255)                            aaCCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGgtg                                                                                                                                                                                                                >  1:236924/1‑251 (MQ=255)                               cTGATCATCGTACTTTTTTAAGAGCACTGGATGGATTCGAAGTTAATGGATTACGATTATTTCGCCTCTCGCTTCCAGAACCTTCAGTTAAAACCCTTTTTGCCGCAAATGAATTTTATCGAAATCATGATGATTTCATAAACCCTCATCTACAAGAACGGTTAGCGCTCGGGGATTATAGCATTTCAATATTTCATTATGACATTAAAGGTGCTGCTGCCAACTTACTGATTTAGTGTCTGATGGTGttt                                                                                                                                                                                                             >  2:125158/1‑251 (MQ=255)                                    tATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCATCTCGATTCCACAACCTTCAGTTAAAAAACTTTTTGCCGTAAATGACTTTTATAGAAATAATGATGATTTCCTAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTg                                                                                                                                                                                                          >  1:156668/1‑249 (MQ=255)                                                         atggatggTTTCGCAGATAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCCGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAACCCCTGATCTACAAGAACGGTTCGTGCTCGGGGATTATAGCCTTTCAATATTTACTTATGACATTACAGGTGATGCTGCCAACTTACTGATTTAGTGTCTGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGttt                                                                                                                                                                                   >  2:159495/1‑251 (MQ=38)                                                         atggatggATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTcc                                                                                                                                                                                                 <  2:477/237‑1 (MQ=255)                                                         atggatggATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTcc                                                                                                                                                                                                 >  1:477/1‑237 (MQ=255)                                                                 atTCGAATTTAATGGATTACGATTATGTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTTCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACTGTTAGTGATCGTGGATTATAGCATTTCAATATTTACTGATGACATTAAAGGTGATGCTGCCAACTTACTGATGTAGTGTATGATGGTGTTTTTGAGGTGGTCCAGTGGCTTCTGTTTCTATCAGc                                                                                                                                                                           <  1:159495/251‑1 (MQ=255)                                                                                                 tctcGATTCCAGAAACTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggtggt                                                                                                                                           >  2:115022/1‑251 (MQ=255)                                                                                                    cGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATGTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGGGTATGATGGTGTTTTTGAGGTTCTCCATTGGCTGCTGGGTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGc                                                                                                                                         <  1:37378/250‑1 (MQ=37)                                                                                                                cTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaaa                                                                                                                              >  1:137818/1‑249 (MQ=255)                                                                                                                        aaaaaCCTTTTTGCCGTAAATGAATTTTAAAGAAATAATGATGATTACATAACCCCTGATCTACAAGAACGGTTAGGGATCGGGGATTATAGCATTTCAAAATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACGGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCGGTGGCTTCTGTTTCTATCATCTGGCCCTCCGTTTCAGCTACTGACGGGGTGGGGCGTACCGGCAAAAGCAccgccg                                                                                                                    <  2:137818/251‑1 (MQ=25)                                                                                                                                      cGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAATGTGATGCTGCCAACTTACTGATTTAGTGTAGGATGGTGTGTGTGATGTGCGCCAGTGGCTTTGGTTGCTATCAGCTGTCCCGCCTGTTCATCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTAt                                                                                                      <  1:280779/251‑1 (MQ=25)                                                                                                                                       gTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTAtc                                                                                                     >  1:241089/1‑251 (MQ=255)                                                                                                                                                                      tCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAAc                                                                       <  1:29314/250‑1 (MQ=255)                                                                                                                                                                          aaaCCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAg                                                                  <  2:236924/251‑1 (MQ=255)                                                                                                                                                                                 gATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTCCTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGGCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGGCGTAAAACATGGCAACTGCAGTTCAc                                                             <  1:264906/249‑1 (MQ=255)                                                                                                                                                                                     tACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTacac                                                       >  1:183552/1‑251 (MQ=255)                                                                                                                                                                                         aGAACGGTTAGTGAGCGGGGATTATAGCATTTCAATATTTACTTATGACAGTAAAGGTGATGCGGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCCCCTGTTCAGTTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCCCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCt                                                   <  2:170829/251‑1 (MQ=255)                                                                                                                                                                                           aaCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTtc                                                 <  1:282313/251‑1 (MQ=255)                                                                                                                                                                                                      aTCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGt                                       >  1:261272/1‑250 (MQ=255)                                                                                                                                                                                                        cGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTGCTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTAGCAGCTGGCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACg                                    <  1:179338/251‑1 (MQ=255)                                                                                                                                                                                                         ggggATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGc                                   >  2:168474/1‑251 (MQ=255)                                                                                                                                                                                                                    cATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATc                        >  2:295893/1‑251 (MQ=255)                                                                                                                                                                                                                             atTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCgg                                        >  1:154074/1‑226 (MQ=39)                                                                                                                                                                                                                             atTTACTTATGACAGTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCgg                                        <  2:154074/226‑1 (MQ=37)                                                                                                                                                                                                                               ttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCACACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATCATTGATATGGc             >  2:232446/1‑251 (MQ=37)                                                                                                                                                                                                                                 aCTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATCATTGATATGGcc            >  1:196918/1‑250 (MQ=35)                                                                                                                                                                                                                                    tATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATCATTGATATGGCCATg         >  1:67848/1‑250 (MQ=34)                                                                                                                                                                                                                                         aagacaaGGGGATGCTGCCAACTTACAGATGTAGTGGAGGCTGGTGGTGTGGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGGCCCTCCGGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGGTCACTTACACCGCGTCTCAACCCGGGACGCACCAGAAAATCATTGATATGGCCATGAATGGc   <  2:109368/246‑1 (MQ=11)                                                                                                                                                                                                                                          aTTAAAGGTGATGCTGCCAACTTCCTGCTTTAGTGCATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGCCGGGGTGGTGCGTAACGGCAAACGCACCGCCGGACCTCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCACCTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCCCCCGCAACTCCTTGATATGGCCCTGACTGGCg  >  2:294799/1‑251 (MQ=11)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                     ATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTATCTCTGCTCTCACTGCCGTAAAACATGGCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCG  >  NC_000913/3583189‑3583672

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ 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.