New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	14 (1.010)	5 (0.410)	5/242	NT	31.0%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	10 (0.820)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GAAAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAATACGCTCAGA  >  USA300TCH1516_ALE/895643‑895933                                                                                                                                               |                                                                                                                                                     gAAAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTcc                                                                                                                                                <  1:50288/149‑1 (MQ=255) gAAAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTcc                                                                                                                                                <  1:259732/149‑1 (MQ=255)                        aagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaata                                                                                                                         >  1:239268‑M1/120‑149 (MQ=255)                                 aaTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATAccc                                                                                                                <  1:176711/149‑1 (MQ=255)                                                 ggACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGAtt                                                                                                >  1:300976/1‑149 (MQ=255)                                                                      aTCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTAt                                                                           <  1:246333/149‑1 (MQ=255)                                                                       tcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTAtt                                                                          >  1:98251‑M1/73‑149 (MQ=255)                                                                          aaGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaa                                                                       <  1:186298/149‑1 (MQ=255)                                                                              aTTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATa                                                                   >  1:225615/1‑149 (MQ=255)                                                                                  aTTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATaaaaa                                                               <  1:40512/149‑1 (MQ=255)                                                                                          gcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAAGAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcaca                                                       <  1:44513‑M1/96‑1 (MQ=255)                                                                                          aTTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcaca                                                       <  1:76114/149‑1 (MQ=255)                                                                                                    caatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAg                                             >  1:1184‑M1/44‑149 (MQ=255)                                                                                                               ttgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGCTATTTTAGTGATCTTGAAAATAAAAAAGGGCACAAAGGGGGCAGTATATGCAAAt                                  <  1:120803‑M1/117‑1 (MQ=255)                                                                                                                         aaTGAAAAATACAATGGTGCAGTTATTCCTGCTAACTAGGTCTTATGGGAGTAAAGTACCCGGTAGGAACAACGAGGAAGGGGTTATTTTTGTTGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAAttt                        <  1:120970/149‑1 (MQ=255)                                                                                                                         aaTGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAAttt                        <  1:46228/149‑1 (MQ=255)                                                                                                                            gAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTaa                     <  1:242801/149‑1 (MQ=255)                                                                                                                                       tGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAATa          <  1:194030/149‑1 (MQ=255)                                                                                                                                         gTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAATACg        >  1:81271/1‑149 (MQ=255)                                                                                                                                               TTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAATACGCTCAGa  >  1:171995‑M1/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                                     GAAAGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAATACGCTCAGA  >  USA300TCH1516_ALE/895643‑895933

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.