New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2085296 =	42 (0.800)	17 (0.360)	10/252	3.4	31.8%	intergenic (‑558/‑400)	mapW2/USA300HOU_1944	cell surface protein MapW2/hypothetical protein
	?	CP000730	= 2128343	35 (0.750)					intergenic (+57/+1062)	int/hlgB	bacteriophage integrase/possible leukocidin subunit
Rejected: Coverage evenness skew score above cutoff.

CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAG  >  CP000730/2128204‑2128481                                                                                                                                            |                                                                                                                                           cTACAACCGGGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAt                                                                                                                                           <  1:336260/141‑1 (MQ=255)      tCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATc                                                                                                                                      <  1:687856/141‑1 (MQ=255)      tCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATc                                                                                                                                      <  1:378145/141‑1 (MQ=255)       ccGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATcc                                                                                                                                     <  1:321466/141‑1 (MQ=255)              ttCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTgg                                                                                                                              <  1:851359/141‑1 (MQ=255)               tctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGGCTCCAAACCCAATAAATACTGTTTTTACAAGGTTTCTATGTATCCAAACTggg                                                                                                                             >  1:311823/1‑141 (MQ=255)                ctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTgggg                                                                                                                            >  1:139951/1‑141 (MQ=255)                ctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTgggg                                                                                                                            >  1:13483/1‑141 (MQ=255)                     ttGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAat                                                                                                                       <  1:315870/141‑1 (MQ=255)                                aaaaTTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCt                                                                                                            >  1:1033236/1‑141 (MQ=255)                                     ttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAttt                                                                                                       >  1:603906/1‑141 (MQ=255)                                           aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTCTGTAATTTAGGTACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                 <  1:514399/141‑1 (MQ=255)                                           aaGAGGAAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                 <  1:721260/141‑1 (MQ=255)                                            agcagACAAAAAAAAACCTAAAATTGTAGAAAGTATGTAACTTAAGCACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGa                                                                                                <  1:130904/137‑1 (MQ=255)                                            agagGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGa                                                                                                <  1:608212/141‑1 (MQ=255)                                             gagGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGAc                                                                                               <  1:291/141‑1 (MQ=255)                                               ggACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACaa                                                                                             >  1:122332/1‑141 (MQ=255)                                               ggACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACaa                                                                                             >  1:629815/1‑141 (MQ=255)                                               ggACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACaa                                                                                             >  1:414574/1‑141 (MQ=255)                                                 aCAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAAtc                                                                                           <  1:824907/141‑1 (MQ=255)                                                   aaaaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAAGGAATGGTATCCCAATAAATGCTGTGGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAAtctt                                                                                         >  1:872804/1‑141 (MQ=255)                                                       aaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTta                                                                                     <  1:560233/141‑1 (MQ=255)                                                          caacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTatat                                                                                  >  1:997663/1‑141 (MQ=255)                                                          caacTAAAATTTTAGAAAGGATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCCATATAAACGCGCTGATTTAATCGGACAATCTTCTTatat                                                                                  >  1:629996/1‑141 (MQ=255)                                                                 aaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaat                                                                           >  1:553709/1‑141 (MQ=255)                                                                   ttttAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCCAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaataa                                                                         <  1:38607/141‑1 (MQ=255)                                                                         aaaGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGt                                                                   >  1:200581/1‑141 (MQ=255)                                                                         aaaGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACCGTTGTTACAAGGTTTAAATGTATGCAAACGGGGGGCAATAGAAACGCGCTGATTGAATTGGACAATCTTCTTATATTAAAAATAATGATGt                                                                   >  1:46146/1‑141 (MQ=255)                                                                             tATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTa                                                               <  1:784595/141‑1 (MQ=255)                                                                                    tttAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATAttaa                                                        >  1:4554/1‑139 (MQ=255)                                                                                     ttAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTCTGTATCCAAACTGGGTGCAATATAAACGCGCGGATTTAATCGGACAATCTTCCTATCTTCAAAATAATGATGTCGTAATCTTcga                                                       >  1:550065/1‑139 (MQ=255)                                                                                             ccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATAAAGCAt                                               >  1:362992/1‑141 (MQ=255)                                                                                               aTTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCAttt                                             <  1:826529/141‑1 (MQ=255)                                                                                                      aCTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATg                                      >  1:853038/1‑141 (MQ=255)                                                                                                       cTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATTGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATgg                                     <  1:943495/141‑1 (MQ=255)                                                                                                            aaCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCGATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCGATGAAGCATTTGATAATGGTGAAt                                >  1:102893/1‑141 (MQ=255)                                                                                                            aaCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCAt                                >  1:480387/1‑141 (MQ=255)                                                                                                               ccAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGACAATATAAACGCGCTGCTTTAATCGGACAATCTTCTTATATTAAAAATAATGAAGTCGTAATATTCAATGACGCATTTGCTATGGGTGCATCAg                             >  1:10959/1‑141 (MQ=255)                                                                                                                                       tttCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATGTTCAATGAAGCATTTGATAATGGTGCATCAGAGAAATTAGTAAGAAATGTGgaaa     >  1:198957/1‑141 (MQ=255)                                                                                                                                          cTATGTATCCAAACTGCGTGCAAGATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATTATGTCCTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAg  <  1:26983/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                           CTACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAG  >  CP000730/2128204‑2128481

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.