New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	26 (1.150)	5 (0.250)	5/244	1.9	18.2%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	22 (1.110)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD
Rejected: Frequency below/above cutoff threshold.

GATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAA  >  USA300TCH1516_ALE/895655‑895923                                                                                                                                   |                                                                                                                                           gATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTga                                                                                                                                   >  1:252581/1‑139 (MQ=255)  aTAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCt                                                                                                                                  >  1:246372/1‑140 (MQ=255)      tCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGATGCAGTTCATCCTGCTAaat                                                                                                                              >  2:198071/1‑140 (MQ=255)         ttATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAaataat                                                                                                                           <  1:154443/140‑1 (MQ=255)          taggCAAACTTAATTGCTGTTAAAGGAGGACATCAAGATGACCAAACAATGTATGCATTAATTGAAGTATTACAATCTAGAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTGTTCCTGCTAAataata                                                                                                                          <  2:254370/137‑1 (MQ=255)            aagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATAcc                                                                                                                        <  1:13679‑M1/21‑1 (MQ=255)                  cTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaa                                                                                                                  >  1:221700/1‑140 (MQ=255)                      aTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaataa                                                                                                              >  1:212450/1‑140 (MQ=255)                               aaaGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCt                                                                                                     <  1:181912/140‑1 (MQ=255)                                   aagGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATAGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaa                                                                                                 <  2:65395/140‑1 (MQ=255)                                             agaagaTAAGAAAATCAAGGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGAt                                                                                       <  1:147099/140‑1 (MQ=255)                                                  atAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGCTTACgg                                                                                  >  1:61718/1‑140 (MQ=255)                                                        aaaTCAAAGCATTAATTGAAGTATTACAATCTAAAGCTATTCAAGACTTCATTAATTAAAAATACAATGATAAACTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATACCAACGATTAAGGGGCTAt                                                                            >  1:86908/1‑140 (MQ=255)                                                              aaGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTtgt                                                                      >  1:42653/1‑140 (MQ=255)                                                                                  cAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAgg                                                  >  2:86169/1‑140 (MQ=255)                                                                                   aaTCTAAAGATATTCAAGACTTCATTAATGAAGACATTGCTAATCGAGATAGGCCTGCTAAATAATATCAATTAAATCCAAATACCTGTTCAGGAAAATGCTTCAAGGGATATTCTTGAGGTCATGAAAATaacacacag                                                 >  2:241446/1‑133 (MQ=255)                                                                                     tCTAAAGATATTCAAGACTTTATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGca                                               <  1:171149/140‑1 (MQ=255)                                                                                     tCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGca                                               <  2:221700/140‑1 (MQ=255)                                                                                        aaatgtttttattgcccttgaccttccttgataagctggctaaTTATTACTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaa                                            >  2:34319‑M1/44‑140 (MQ=255)                                                                                         aatgttttaaaggaccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaa                                           >  2:156315‑M1/43‑140 (MQ=255)                                                                                          atgtgttgattgccctggaacttccttgataatctggctaaTTATTCCTGCTAAATAAGACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                          >  2:111001‑M1/42‑140 (MQ=255)                                                                                          aGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                          >  1:55313/1‑140 (MQ=255)                                                                                           gATATTCAAGACTGCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAg                                         <  2:217144/140‑1 (MQ=255)                                                                                            gttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAgg                                        <  2:73569‑M1/101‑1 (MQ=255)                                                                                                    gACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGtat                                >  2:85984/1‑140 (MQ=255)                                                                                                                      tACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAAttt              >  2:74488/1‑140 (MQ=255)                                                                                                                       aCAATGGTGCAGTTATTCCTGCTAAATAATACCAATCAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAAtttt             >  1:249880/1‑140 (MQ=255)                                                                                                                        cAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGACAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTa            >  2:172112/1‑140 (MQ=255)                                                                                                                          aTGGTGAAGTTATTCCGTCTAAAAAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGTTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTaaa          <  2:252581/140‑1 (MQ=255)                                                                                                                               gCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAACTTATCGAATTTTAAACaaaa     >  1:88840/1‑140 (MQ=255)                                                                                                                                  gTTATTCCTGCTAAATAATACAAATTAAATAACAATACAATTTAATAACAACGAAAAAGGGGTTATTTTCGTAGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATCACCGAATTTTAACCaaaaaga  >  2:13274/1‑138 (MQ=255)                                                                                                                                   |                                                                                                                                           GATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAA  >  USA300TCH1516_ALE/895655‑895923

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.