New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 2491587	23 (0.600)	8 (0.220)	5/292	NT	27.4%	coding (188/1239 nt)	alaC	valine‑pyruvate aminotransferase 3
	?	CP009273	= 2491794	21 (0.590)					intergenic (‑20/‑356)	alaC/ypdA	valine‑pyruvate aminotransferase 3/sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system

ACCAGCGGCACTGAGCGTACCTGCGCCCCGGCAATCACCGCGCCATAAATATGGATCGGGTAACTTGGATTCGGCACCAGCACCGTGTCACCATGATCCAGCGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAATCGATAATATCTTCGCCGCGCCGACGCGCAGCCATTTTCAGTTCAGCGGTGATGTTAAAAACGTAGGGCGGGAGACGATCAATGCGCGTAAAGCGACGTTCAGGGCGAGTGTCAGCCATAATTTCCTCAGATTAACGTTAGCGCCCGGACCGTCCGAGCGAC  >  CP009273/2491320‑2491817                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                       accaGCGGCACTGAGCGTACCTGCGCCCCGGCCATCCCCGCGCCATAAATATGGATCGGGTAACTTGGATTCGGCACCAGCACCGTGTCACCATGATCCAGCGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCca                                                                                                                                                                                                                                  <  1:585700/274‑1 (MQ=255)                                                      gATCGGGTAACTTGGATTCGGCACCAGCACCGTGTCACCATGATCCAGCGGCGCCAGCATCAGATTCGCCAGGCCCTCTTTCGAACCACTAGTTACCGTGGCCTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATACTGAGACCCGCAGGAAATGGCGCGACGTAACCGCGGAATGCCGGGTGAAGTGGCGTAACCCTGCCTGTCCGAGAGATGAGCCCCAGTCCATAATTTTTTTCCCCTCTTCGGCGGAGCTGCCCCGCGCGGGTTAcctc                                                                                                                                                                            >  2:299376/1‑273 (MQ=255)                                                                 tgggaaaaaaatgcAGGACAGTGTGACCCTGATCCAGCGTCGCAAGCATCAGATGCGCCATGCCCTCTTTCGAACCAAGTGGGACGATGGCTTCTGATTCCGGGTCGATTTCAGCGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGTCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAAt                                                                                                                                                                   <  2:565355/260‑1 (MQ=255)                                                                           cACCAGCACCGTGTCACCATGATCCAGCTTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTCAAGTGGAGTAACCATGCGTNGCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGGTACCCATGCTg                                                                                                                                                                       >  1:565364/1‑259 (MQ=255)                                                                              cAGCACCGTGTCACCATGATCCAGCGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAANGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGt                                                                                                                                                                                                >  1:599947/1‑231 (MQ=255)                                                                                  aCCGTGTCACCATGATCCAGCGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCa                                                                                                                                                                                            <  2:599938/231‑1 (MQ=255)                                                                                           ccATGATCCAGCGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAATCGATAATAGATTCGCCGCGCCGAcgcg                                                                                                                                        >  1:145734/1‑274 (MQ=255)                                                                                                aTCCAGCGTCGCCAGCATCAGATGCGCCACGCCCTCTTTCGAAACAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCCACGTCGTAGCGCTCCTGATACCCTCGGGAAATGGCGCGACGTAACCGCGGACTGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATCAGTTTTCGACGCTATGCGACGAAATCTCATCAGCCGTGTTACCCATTCTGAAGTCGATACTCTATTctccgcgccaccgcctagt                                                                                                                                    >  2:330189/1‑263 (MQ=255)                                                                                                      cGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTACCCATGCGTGTNCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAATCGATAATATCTTCGCCGCGCCGACGCGCAGCCATTtcca                                                                                                                            >  1:662817/1‑275 (MQ=255)                                                                                                      cGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCa                                                                                                                                                                                            >  2:600098/1‑211 (MQ=255)                                                                                                          gCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCCACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGt                                                                                                                                                                                        <  1:600107/211‑1 (MQ=255)                                                                                                          gCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTggg                                                                                                                                                                                                                                     <  2:380187/166‑1 (MQ=255)                                                                                                                                            cAATAGGGACGATGGCTTCTGATTCCGGGTCTATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGGTGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAATCGATAATATCTTCGCCGCGCCGACGCGCAGCCATTTTCAGTTCAGCGGTGATGTTAAAAACGTAGGGCGGGAGACg                                                                                       <  1:437351/274‑1 (MQ=255)                                                                                                                                                    gcGATGGCTTCTGATTCCGGGTCGATTTCAACGTGGTAGCGATCCTGATACAAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAATCGATAATATCTTCGCCGCGCCGACGCGCAGCCATTTTCAGTTCAGCGGTGATGTTAAAAACGTAGGGCGGGAGACGATCAATgc                                                                               <  1:330195/273‑1 (MQ=255)                                                                                                                                                         ggCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTgg                                                                                                                                                                                                                                      >  1:614190/1‑118 (MQ=255)                                                                                                                                                             tCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCca                                                                                                                                                                                                                                  <  2:614181/118‑1 (MQ=255)                                                                                                                                                                                       gtAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTaacgttaatctgaggaaattatggctgacactcgccctgaacgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgc                                                                                                                                          >  1:301583‑M1/1‑86 (MQ=255)                                                                                                                                                                                           cGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTaacgttaatctgaggaaattatggctgacactcgccctgaacgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgctgaa                                                                                                                                      <  2:301577‑M1/180‑99 (MQ=255)                                                                                                                                                                                              tCCTGATACCAGCTGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTaacgttaatctgacgaaattatggctgaccctcgccctgaacgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgctgaactgaaaatggctgcgcgtcggcgcggcgaagatattatcgatttcagcatgggtaacccggacggggcgactccgccgcatatcgtcgaaaaattatg                                    <  1:169154‑M1/275‑197 (MQ=255)                                                                                                                                                                                              tCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGTAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTaacgttaatctgaggaaattatggctgacactcgccctgaacgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgctgaactgaaaatggctgcgcgtcggcgcggcgaagatattatcgatttcagcatgggtaacccggacggtgcgactccgccgcatatcgtcgaaaaattatg                                    <  1:449496‑M1/275‑197 (MQ=255)                                                                                                                                                                                              tCCTGATACCAGCGGGAAATGGCGCGAAGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTaacgttaatctgnggaaattatggctgacactagccctgaccgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgctgaactgaaaatggctgcgcgtcggcgcggcgaagatattatcgatttcagcatgggtaacccggacggtgcgcctccgccgcatatcgtcgaaaaattatg                                    <  1:552835‑M1/275‑197 (MQ=255)                                                                                                                                                                                                cTGATTACAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTaacgttaatctgaggaaattatggctgacactcgccctgaacgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgctgaactgaaaatggctgcgcgtcggcgcggcgaagatattatcgatttcagcatgggtaacccggacggtgcgactccgccgcatatcgtcgaaaaattatgta                                  <  1:432201‑M1/275‑199 (MQ=255)                                                                                                                                                                                                cTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAATCGATAATATCTTCGCCGCGCCGACGCGAAGCCATTTTCAGTTCAGCGGTGATGTTAAAAACGTAGGGCGGGAGACGATCAATGCGCGAAAAGCGACGTTCAGGGCGAGTGGCAGCCATAAtttacca                                    >  2:319151/1‑269 (MQ=255)                                                                                                                                                                                                          ggggAGATGGCCCGACGGAGCCGCGTGATGCCGCGTGAAGTGGAGTAGCCTTGCGTGTTCGTGCTCTGGGGCACATGACGTAATTGTTCGACGGTATGCGGCGGGGTGTCACCGTCCGGGTTACCCATGCTGAAACCGATAATATCTGCGCCGCGCCGATGCGCAGCCATTTTCAGTGCAGCGGTGATGTTAAAAGCGTAGGGCGGGAGACGATCAATGCGCGTAAAGCGACGTTCAGGGCGAGTGTCAGCCATAATTTCCTCAGATTAACGtt                         <  2:662808/273‑1 (MQ=255)                                                                                                                                                                                                                 tGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTgg                                                                                                                                                                                                                                      >  2:568037/1‑62 (MQ=255)                                                                                                                                                                                                                    cgcgACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGt                                                                                                                                                                                  >  1:542373/1‑111 (MQ=255)                                                                                                                                                                                                                     gcgACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCca                                                                                                                                                                                                                                  <  1:568046/62‑1 (MQ=255)                                                                                                                                                                                                                        aCGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGCTTAcc                                                                                                                                                                              <  2:542364/111‑1 (MQ=255)                                                                                                                                                                                                                                 cgGATTGCCGCGTGAAGTGTGTTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTGCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTAAAATCGATAATATCTTCGCCGCGCCGACGCGCAGCCATTTTCAGTTCAGCGGTGATGTTAAAAACGTAGGGCGGGAGACGATCAATGCGCGTAAAGCGACGTTCAGGGCGAGTGTCAGCCATAATTTCCTCAGATTAACGTTAGCGCCCGGACCGTCCGAGCGAc  <  1:319157/274‑1 (MQ=255)                                                                                                                                                                                                                                 cgGAATGCCGCGTGAAGTGGAGTCACCATGCGTGTCCGGGCGCTaacgttaatctgaggaaattatggctgacactcgccctgaacgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgctgaactgaaaatggctgcgcgtcggcgcggcgaagatattatcgatttcagcatgggtaacccggacggtgcgactccgccgcatatcgtcgaaaaat                                        >  1:492405‑M1/1‑44 (MQ=255)                                                                                                                                                                                                                                     aTGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTaacgttaatctgaggaaattatggctgacactcgccctgaacgtcgctttacgcgcattgatcgtctcccgccctacgtttttaacatcaccgctgaactgaaaatggctgcgcgtcggcgcggcgaagatattatcgatttcagcatgggtaacccggacggtgcgactccgccgcatatcgtcgaaaaattatg                                    <  2:492398‑M1/236‑197 (MQ=255)                                                                                                                                                                                                                                                              gCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCCCCGTCCGGGTTACACATGCTGAAATCGATAATATCTTCGACGCGCCGACGCGCAGCCATTTTCAGTTCAGCGGTGATGTTAAAAACGTAGGGCGGGAGACGATCAATGCGCGTAAAGCGACGTTCAGGGCGAGTGTCAGCCATAATTTCCTCAGATTaa                             >  1:283282/1‑218 (MQ=255)                                                                                                                                                                                                                                                                   tCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCa                                                                                                                                                                                            >  2:193670/1‑54 (MQ=255)                                                                                                                                                                                                                                                                       ggCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGt                                                                                                                                                                                        <  1:193673/54‑1 (MQ=255)                                                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                       ACCAGCGGCACTGAGCGTACCTGCGCCCCGGCAATCACCGCGCCATAAATATGGATCGGGTAACTTGGATTCGGCACCAGCACCGTGTCACCATGATCCAGCGTCGCCAGCATCAGATGCGCCAGGCCCTCTTTCGAACCAATAGTGACGATGGCTTCTGATTCCGGGTCGATTTCAACGTCGTAGCGATCCTGATACCAGCGGGAAATGGCGCGACGTAACCGCGGAATGCCGCGTGAAGTGGAGTAACCATGCGTGTCCGGGCGCTGGGCCACAGTACATAATTTTTCGACGATATGCGGCGGAGTCGCACCGTCCGGGTTACCCATGCTGAAATCGATAATATCTTCGCCGCGCCGACGCGCAGCCATTTTCAGTTCAGCGGTGATGTTAAAAACGTAGGGCGGGAGACGATCAATGCGCGTAAAGCGACGTTCAGGGCGAGTGTCAGCCATAATTTCCTCAGATTAACGTTAGCGCCCGGACCGTCCGAGCGAC  >  CP009273/2491320‑2491817

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ 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.