New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	671622 =	47 (1.240)	5 (0.140)	5/256	4.4	9.8%	intergenic (+247/‑141)	argS/USA300HOU_0614	arginine‑‑tRNA ligase/deoxyribonuclease (pyrimidine dimer)
	?	CP000730	= 1072271	47 (1.300)					intergenic (‑743/+62)	iraE/folD	possible chitinase/bifunctional methylenetetrahydrofolate dehydrogenase (NADP(+))/methenyltetrahydrofolate cyclohydrolase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGACTTTATTAAAACTCAGTTATTAGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTAATTGTTAATGGACCAAC  >  CP000730/1072143‑1072410                                                                                                                                 |                                                                                                                                            aGACTTTATTAAAACTCAGTTATTAGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTg                                                                                                                                 >  1:334643/1‑141 (MQ=255)            aaaCTCAGTTATTAGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACt                                                                                                                      <  1:299268/141‑1 (MQ=255)                  aGTTATTAGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCGCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTag                                                                                                                >  1:123047/1‑141 (MQ=255)                  aGTTATTAGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTag                                                                                                                >  1:319362/1‑141 (MQ=255)                   gTTATTAGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTaga                                                                                                               <  1:196027/141‑1 (MQ=255)                    ttattaGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTagag                                                                                                              >  1:285288/1‑141 (MQ=255)                               agttaCAGAAATGATATTTTCGTATAATTTATTTCGTCGTGGTTCTTCTTCAAGTTTGAATAAAAATGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACAtt                                                                                                   <  2:130445/137‑1 (MQ=14)                                 ggACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGa                                                                                                 >  2:340878/1‑141 (MQ=255)                                  gACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGAt                                                                                                <  2:343941/141‑1 (MQ=255)                                  gACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGAt                                                                                                <  1:256870/141‑1 (MQ=255)                                   aCAGAAAGGATATTTTCGTAAAATTTATTTCGTGGTCACACCCCGGCAAGCTTGACAAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGAtt                                                                                               >  2:60563/1‑141 (MQ=14)                                       aaaTGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATg                                                                                           >  2:128025/1‑141 (MQ=255)                                           gatatctgctcaaaaTTTATTTCCTCGTCCCACCCCGGCAATGTTGACGAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGtctc                                                                                       <  1:355392/130‑1 (MQ=11)                                           gATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGtctc                                                                                       >  1:36635/1‑141 (MQ=255)                                            atatTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCa                                                                                      >  1:242742/1‑141 (MQ=255)                                                tttCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGct                                                                                  >  2:29636/1‑141 (MQ=255)                                                  tCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGctct                                                                                <  2:250474/141‑1 (MQ=255)                                                         atttatttCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATATAACATTGATTTATGTCTCAGGCTCTTTACGaa                                                                         >  1:207949/1‑141 (MQ=255)                                                         atttatttCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGaa                                                                         >  1:315713/1‑141 (MQ=255)                                                           ttatttCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTGAACATTGATTTATGTCTCAGGctctctatatggc                                                                       <  1:408311/141‑10 (MQ=11)                                                             atttCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCaa                                                                     >  2:411585/1‑141 (MQ=255)                                                               ttCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATa                                                                   >  1:188669/1‑141 (MQ=255)                                                               ttCGTCGTCCCACCCCGGCAAGGTTGACTAGAATCGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATa                                                                   >  2:72034/1‑141 (MQ=255)                                                                       cccACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACg                                                           <  1:236387/141‑1 (MQ=255)                                                                        ccACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTGTACGc                                                          >  2:362166/1‑141 (MQ=255)                                                                        ccACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGc                                                          <  1:168372/141‑1 (MQ=255)                                                                        ccACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATCTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGc                                                          <  2:298622/141‑1 (MQ=255)                                                                          aCCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTATCGTTCAGTCAACTACTGCCATTATAACTTTATCGAGCATAACACATATATCTATATCTCACGCTCTTTACGAATCAATAACTCGACGCAt                                                        >  2:397162/1‑141 (MQ=17)                                                                            cccGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCAttt                                                      <  2:71971/141‑1 (MQ=255)                                                                                 cAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCt                                                 <  2:242742/141‑1 (MQ=255)                                                                                  aaGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTg                                                >  1:400572/1‑141 (MQ=255)                                                                                         aCTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTgcaagcaa                                         <  1:29636/141‑1 (MQ=255)                                                                                            aGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGt                                      <  2:123532/141‑1 (MQ=255)                                                                                            aGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGt                                      <  1:60563/141‑1 (MQ=255)                                                                                              aaTTGAAAAAAGCTTGTTACCAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCACTACCTCGACGCATTTTTTCTGCAACCAAAGtat                                    >  2:360149/1‑141 (MQ=255)                                                                                                  gAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTattatt                                <  2:261969/141‑1 (MQ=255)                                                                                                   aaaaaaGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTAttt                               <  1:340878/141‑1 (MQ=255)                                                                                                   aaaaaaGCTTGTTACAAACGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTgcaagcgtcatcatcctg                               >  2:54213/1‑129 (MQ=18)                                                                                                      aaaGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTGTTTACGAATCAATACCTCGCCGCATTTTTTCTACAAGCAAAGTATTATTTAAt                            >  2:230308/1‑141 (MQ=255)                                                                                                         gCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATAcc                         >  1:158012/1‑141 (MQ=255)                                                                                                            tgctACAAGCGACTTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATa                      <  2:384256/138‑1 (MQ=255)                                                                                                               tACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTa                   >  1:335766/1‑141 (MQ=255)                                                                                                                 cAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTAAt                 <  2:145393/141‑1 (MQ=255)                                                                                                                   aGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTAATTg               <  2:303545/141‑1 (MQ=255)                                                                                                                              gTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTAATTGTTAATGGACCa    <  1:411585/141‑1 (MQ=255)                                                                                                                               ttCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTAATTGTTAATGGACCaa   <  2:212905/141‑1 (MQ=255)                                                                                                                                tCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTAATTGTTAATGGACCAAc  <  2:285288/141‑1 (MQ=255)                                                                                                                                 |                                                                                                                                            AGACTTTATTAAAACTCAGTTATTAGGGAGTGGGACAGAAATGATATTTTCGTAAAATTTATTTCGTCGTCCCACCCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGAATTTTCGTTCAGTCAACTACTGCCATTATAACTTTGTAGAGCATAGAACATTGATTTATGTCTCAGGCTCTTTACGAATCAATACCTCGACGCATTTTTTCTGCAAGCAAAGTATTATTTAATACCATAGTAATTGTTAATGGACCAAC  >  CP000730/1072143‑1072410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.