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

ATGGCTATTGTTGGCTCACCGGATTATTTTTCTCGCCGAAGTGTTCCAACGTCAGTGTCACAATTAATAGATCATCAGGCAATTAATTTGTATCTTCCCACATCGGGTACAGCAAATCGCTGGAGATTAATACGCGGTGGACGTGAAGTTCGTGTTCGCATGGAAGGTCAGCTTTTACTGAATACGATAGACCTGATCATTGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGC  >  CP009273/1386743‑1387240                                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                         gagtgcttcataagtttccctctaaccgacattaaaattgatgcgtaattatttgtttcgccttaaagaaatgcaaacaacttccatcaaaaaagtgacaaaggaagcatcaaatgttttaagtatcaatatatcaaatcagatttagtgtaaataatagtctccaaaatgcggtaaagcacatagaactccgaacactacgttagggcttcgcacgttcaaaaccgttatcggtatcataaccagcagctgtcgccattntaccaaaaaaaaaa                                                                                                                                                                                                                                 <  2:517257‑M1/10‑1 (MQ=255)                                       tgatgcgtaattatttgtttcgccttaaagaaatgcaaacaacttccatcaaaaaagtgacaaaggaagcatcaaatgttttaagtatcaatatatcaaatcagatttagtgtaaataatagtctccaaaatgcggtaaagcacatagaactccgaacactacgttcgggcttcgcacgttcaaacccgttttcggtatcataatcagcatctgtcgccattgtacga                                                                                                                                                                                                                                          >  1:603363‑M1/228‑228 (MQ=255)                                                                    tAGATCATCAGGCAATTAATTTGTATCTTCCCACATCGGGTACAGCAAATCGCTGGAGATTAATACGCGGTGGACGTGAAGTTCGTGTTCGCATGGAAGGTCAGCTTTTACTGAATACGATAGACCTGATCATTGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTaa                                                                                                                                                                                                                                          <  2:352934/199‑1 (MQ=255)                                                                                                tCCCACATCGGGTACAGCAAATCGCTGGAGATTAATACGCGGTGGACGTGAAGTTCGTGTTCGCATGGAAGGTCAGCTTTTACTGAATACGATAGACCTGATCATTGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATAAGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACATGTACTATCCACACCGCAGACCAGCGGTCTGGGCTTtctcggggt                                                                                                                                  >  2:563092/1‑270 (MQ=255)                                                                                                               aGCAAATCGCTGTATATTAATACGTGTTGGACGTGAAGTTCGTGTTCGCATGGAAGGTCAGCTTTTACTGAATACGATAGACCTGATCATTGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGTGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTg                                                                                                                    <  1:171609/274‑1 (MQ=255)                                                                                                                gCAAATCGCTGGAGATTAATACGCGGTGGACGTGAAGTTCGTGTTCGCATGGAAGGTCAGCTTTTACTGAATACGATAGACCTGATCATTGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATAAGTGTTTTGGATAAATTCACACCAGATTTACCAGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTGATTATTTACACATAGGATg                                                                                                                    >  2:171607/1‑273 (MQ=255)                                                                                                                                                                                               aCCTGATCATTGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAAc                                   >  1:114488/1‑275 (MQ=255)                                                                                                                                                                                                        ttGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTaa                                                                                                                                                                                                                                          <  2:542127/67‑1 (MQ=255)                                                                                                                                                                                                         tGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATc                                                                                                                                                                                  >  2:279559/1‑122 (MQ=255)                                                                                                                                                                                                             gctgcAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCt                                                                                                                                                                              <  1:279563/122‑1 (MQ=255)                                                                                                                                                                                                              ctgcAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTAccc                                                                                                                                                                                         >  2:69768/1‑110 (MQ=255)                                                                                                                                                                                                               ggcttcgaacgttcaaacccgttttcggtatcataatcagcatctgtcgccattgtacgAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCAGGAGATCACCTGTAATATCCACACCGTCGACATGCTGGCACGGCATTCACATTATTGatagatag                                                                                                                        <  2:145954‑M1/115‑1 (MQ=255)                                                                                                                                                                                                                  aaTTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGtt                                                                                                                                                                                     <  1:69769/110‑1 (MQ=255)                                                                                                                                                                                                                   tcgcacgttcaaacccgttttctgtatcataatcagcatctgtcgccattgtacgAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTATACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGTCTg                                                                                                                    >  1:145955‑M1/56‑174 (MQ=255)                                                                                                                                                                                                                   tcgcacgttcaaacccgttttcggtatcataatcagcatctgtcgccattgtacgAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTg                                                                                                                    >  2:285095‑M1/56‑174 (MQ=255)                                                                                                                                                                                                                          ttcaaacccgttttcggtatcataatcagcatctgtcgccattgtacgAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTatagatag                                                                                                                        <  1:277490‑M1/115‑1 (MQ=255)                                                                                                                                                                                                                              aacccgttttcggtatcataatcagcatctgttgccattgtacgAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTg                                                                                                                    >  2:277486‑M1/45‑163 (MQ=255)                                                                                                                                                                                                                                gtttgtgttATTTAACTTTTGTTTAGTTTGAGCGTGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGANATGCTGGCTCGGAATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGc  <  1:563101/267‑1 (MQ=255)                                                                                                                                                                                                                                                      tCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTc                                                                                                                                                                                                        >  2:24610/1‑55 (MQ=255)                                                                                                                                                                                                                                                          gTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCacac                                                                                                                                                                                                    <  1:24611/55‑1 (MQ=255)                                                                                                                                                                                                                                                              aGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTAccc                                                                                                                                                                                         >  2:368100/1‑62 (MQ=255)                                                                                                                                                                                                                                                                cGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATCGATAGGCTGAAGTATAAAGGTGCTGTTTAGCact                                                                                           >  2:468270/1‑154 (MQ=255)                                                                                                                                                                                                                                                                  ggCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGtt                                                                                                                                                                                     <  1:368104/62‑1 (MQ=255)                                                                                                                                                                                                                                                                    cTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATTCTGCCTCGGCATTCTCATTATTTATAGATTGGCTGAACTATAAAGGTGCTGTTTAGCACTACtt                                                                                       <  1:468277/154‑1 (MQ=255)                                                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                         ATGGCTATTGTTGGCTCACCGGATTATTTTTCTCGCCGAAGTGTTCCAACGTCAGTGTCACAATTAATAGATCATCAGGCAATTAATTTGTATCTTCCCACATCGGGTACAGCAAATCGCTGGAGATTAATACGCGGTGGACGTGAAGTTCGTGTTCGCATGGAAGGTCAGCTTTTACTGAATACGATAGACCTGATCATTGATGCTGCAATTGATGGGCATGGATTGGCGTATCTACCTTATGATCAGGTTGAGCGGGCTATTAAAGAAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGC  >  CP009273/1386743‑1387240

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 23 ≤ 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.