New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1387008 =	17 (0.500)	6 (0.180)	4/314	2.4	20.9%	coding (761/900 nt)	pgrR	murein peptide degradation regulator
	?	CP009273	1387230 =	29 (0.870)					intergenic (+83/‑254)	pgrR/mppA	murein peptide degradation regulator/murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit

GATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACTAAATCTGATTTGATATATTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTC  >  CP009273/1386966‑1387494                                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                                         gtttgtgttATTTAACTTTTGTTTAGTTTGAGCGTGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGANATGCTGGCTCGGAATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGc                                                                                                                                                                                                                                                                <  1:563101/267‑1 (MQ=255)                                                                   tGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTGGAACGTGCGAAGCCCGAACGTAGTGttggtag                                                                                                                                                                                              >  2:592395/1‑270 (MQ=255)                                                                                                                        cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGa                                                                                                                                                                                                                                                              >  2:103841/1‑158 (MQ=255)                                                                                                                            aTGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGa                                                                                                                                                                                                                                                          <  1:103842/158‑1 (MQ=255)                                                                                                                                         tttttaattattTATAGATAGGCTTAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGTTACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACTAAATCTGATTTGATATATTGATACTTaa                                                                                                                        <  2:114487/269‑1 (MQ=255)                                                                                                                                                  cagcctatctataaataatgagaatgccgagccagcatgtcgacggtgtggatagtacaggtgataaccgggtaaatctggtgtgaatttatccaaaacacgtatcagttttttttcttCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGa                                                                                                                                                                                                                    >  2:285095‑M2/120‑174 (MQ=255)                                                                                                                                                  cagcctatctataaataatgagaatgccgagccagcatgtcgacggtgtggatagtacaggtgataaccgggtaaatctggtgtgaatttatccaaaacacgtatcagttttttttcttCGTACAATGGCAACAGATGCTGATTATGATACCGAAAACGGGtt                                                                                                                                                                                                                               >  2:277486‑M2/120‑163 (MQ=255)                                                                                                                                                  cagactatctataaataatgagaatgccgagccagcatgtcgacggtgtggatagtataggtgataaccgggtaaatctggtgtgaatttatccaaaacacgtatcagttttttttcttCGTACAATGGCGACAGATGCTGATTATGATACAGAAAACGGGTTTGAACGTGCGa                                                                                                                                                                                                                    >  1:145955‑M2/120‑174 (MQ=255)                                                                                                                                                    ttatAGATATGCTTAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTNCGTACAATGGTTACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACTAAATCTGATTTGATATATTGATACTTAAAACATTTGATg                                                                                                             <  1:592404/275‑1 (MQ=255)                                                                                                                                                      ctatctatcaataatgtgaatgccgtgccagcatgtcgacggtgtggatattacaggtgatctcctggtaaatctggtgtgaatttatccaaaacacgtatcagttttttttcttCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTTCGAAGcc                                                                                                                                                                                                                <  2:145954‑M2/59‑1 (MQ=255)                                                                                                                                                      ctatctataaataatgagaatgccgagccagcatgtcgacggtgtggatagtacaggtgataaccgggtaaatctggtgtgaatttatccaaaacacgtatcagttttttttcttCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGaa                                                                                                                                                                                                                           <  1:277490‑M2/48‑1 (MQ=255)                                                                                                                                                       tggatagGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCAttt                                                                                                                                                                        >  2:13768/3‑213 (MQ=255)                                                                                                                                                           tagGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGga                                                                                                                                                                    <  1:13769/213‑1 (MQ=255)                                                                                                                                                             ggCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGCGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACAATAAATCTGATTTGATATATTGATACTTAAAACATTTGATGCTTCCTTTg                                                                                                    >  1:259581/1‑275 (MQ=255)                                                                                                                                                              gCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGa                                                                                                                                                                                                                                                          >  1:188395/1‑124 (MQ=255)                                                                                                                                                                  aaGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCt                                                                                                                                                                                                                                                      <  2:188393/124‑1 (MQ=255)                                                                                                                                                                        aaaGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCGTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTATTGTTCGGAGTTCTATGTGNTTTACCGCATTTTGGAGACTATTATTTAAACTAAATCTGATTTGATATATTGATTCTTAAAACATTTGATGCTTCCTTTTTCAATTTTTTg                                                                                         >  1:517265/1‑275 (MQ=255)                                                                                                                                                                                      gCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGc                                                                                                                                                                                    >  2:558004/1‑170 (MQ=255)                                                                                                                                                                                          tactTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTa                                                                                                                                                                                <  1:558013/170‑1 (MQ=255)                                                                                                                                                                                            ctTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATg                                                                                                                                                                                                                                                                  >  2:134875/1‑86 (MQ=255)                                                                                                                                                                                            ctTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGa                                                                                                                                                                                                             >  2:276918/1‑139 (MQ=255)                                                                                                                                                                                               gCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACa                                                                                                                                                                                                                                                            >  2:263504/1‑89 (MQ=255)                                                                                                                                                                                                cTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGa                                                                                                                                                                                                                                                              <  1:134876/86‑1 (MQ=255)                                                                                                                                                                                                cTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGt                                                                                                                                                                                                         <  1:276922/139‑1 (MQ=255)                                                                                                                                                                                                   aTACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                                                                                                                                                                                                                                        <  1:263508/89‑1 (MQ=255)                                                                                                                                                                                                         taatttaattCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGCGCGAAGCCCGACCGTAGTGTTCGGAGTTCTATGTGCTTTACCGAATTTTGGAGACTATTATTTACACTAAATCTGCTTTGATATATTGATCCTTACAACATTTGATGCTTCCTTTGTCACTTTTTTTATGGAAGTTGTTTGCATTTCTTTAAGGCGaaa                                                         >  1:138760/1‑274 (MQ=255)                                                                                                                                                                                                           atttaattCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACg                                                                                                                                                                                                                         >  2:321859/1‑112 (MQ=255)                                                                                                                                                                                                               aattCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCg                                                                                                                                                                                                                     <  1:321863/112‑1 (MQ=255)                                                                                                                                                                                                                     tctcTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGa                                                                                                                                                                                                                                                          >  2:573768/1‑69 (MQ=255)                                                                                                                                                                                                                         ttAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCt                                                                                                                                                                                                                                                      <  1:573777/69‑1 (MQ=255)                                                                                                                                                                                                                                           cTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGtt                                                                                                                                                                                            >  2:597089/1‑109 (MQ=255)                                                                                                                                                                                                                                           cTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTa                                                                                                                                                        >  1:540147/1‑145 (MQ=255)                                                                                                                                                                                                                                               cAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTAt                                                                                                                                                                                        <  1:597098/109‑1 (MQ=255)                                                                                                                                                                                                                                               cAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACt                                                                                                                                                    <  2:540138/145‑1 (MQ=255)                                                                                                                                                                                                                                                               ttttttttttGGTANAATGGCGACAGCTGCTGGTTATGATACCGATAACGGTTTTGAACGTGCGAAGCCCTAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACTAAATCTGATTTGATATATTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCActc  <  2:517257‑M2/265‑1 (MQ=255)                                                                                                                                                                                                                                                                        tCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACTAAATCTGATTTGATATATTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCa                                        >  1:603363‑M2/2‑228 (MQ=255)                                                                                                                                                                                                                                                                         cGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGga                                                                                                                                                                    >  2:129066/1‑103 (MQ=255)                                                                                                                                                                                                                                                                         cGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACTAAATCTGATTTGATATATTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGttt                                                                            >  1:495241/1‑191 (MQ=255)                                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                                         GATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGTGCGAAGCCCGAACGTAGTGTTCGGAGTTCTATGTGCTTTACCGCATTTTGGAGACTATTATTTACACTAAATCTGATTTGATATATTGATACTTAAAACATTTGATGCTTCCTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTC  >  CP009273/1386966‑1387494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ 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.