New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	14 (0.760)	11 (0.690)	10/222	0.5	46.7%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	13 (0.810)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GGGCAAAAAAAGGGCATAATTTTGAAACAAAGG‑GCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATAT  >  USA300TCH1516_ALE/909613‑909867                                                                                                                                 |                                                                                                                                gggCTAAAAATGTGCATAATTTTGAAACAAAGT‑GCAAGGGTATGAATAATAAGGTATCCAAATAACTTTATATATGCATATATAATAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAat                                                                                                                                <  2:2332/129‑1 (MQ=255) gggCAAAAAAAGGGCATAATTTTGAAACAAAGG‑GCAAGGGTATGAATAATAAATTATCTTGGAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTAAACTTCCTTGATAATCTGGCTAAt                                                                                                                                <  2:154818‑M2/129‑2 (MQ=255) gggCAAAAAAAAGACTGACCTGTGAGACAAAGGTGCAA‑GCTATGAATAATAAATTATCTTTGAAATTTTATAAATGCATTTATAACAATGTTTTGATTCCCCTTGAACTACCTTGATAATATGCCTAat                                                                                                                                >  2:156397/1‑129 (MQ=255)        aaaaGGGGATGAGTTGGAAACACCTG‑GTAAAGGTATGAATAATAAATTATCTTGAATAGTTTATCAATGCATATATTATAATTTTTTGATGGTCCTTGAACTTCCTTGATAATCTGGTTAATTATTCCt                                                                                                                         <  2:12161/129‑1 (MQ=255)           aGGGCATAATTTTGAAACAAAGG‑GCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCACTTGAACTTCCTTAATAATCTGGCTAAttattcctgct                                                                                                                      <  2:111484‑M2/129‑12 (MQ=255)            gggCATAATTTTGAAACAAAGG‑GCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgcta                                                                                                                     <  2:137261‑M2/129‑13 (MQ=255)               cATAATTTTGAAACAAAGG‑GCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATCGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaat                                                                                                                  <  1:131945‑M2/129‑16 (MQ=255)                          aaCAAAGG‑GCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCGCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTa                                                                                                       <  1:166606/129‑1 (MQ=255)                               aGG‑GCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGc                                                                                                  <  1:176866/129‑1 (MQ=255)                                       gtgTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGATCTTCCTTGATAATCTGGCTAATTATTCCTGCTAAAGAAATCATATTAATGGCTCAGTaa                                                                                           <  1:38202/127‑1 (MQ=255)                                           aTGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTg                                                                                       <  2:41015/129‑1 (MQ=255)                                             gAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGAt                                                                                     <  2:205634/129‑1 (MQ=255)                                             gAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGAt                                                                                     >  2:191730/1‑129 (MQ=255)                                                  attaaTTATCTTGATAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGTTCAGTAACGTGATGTTGc                                                                                <  2:101642/126‑1 (MQ=255)                                                                 aaTTTTATAAATGCATATATAACAATGTTTTGATCGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggtta                                                                 >  2:131945‑M2/1‑65 (MQ=255)                                                                            tGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataatacaaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggta                                                      <  1:55505‑M2/129‑76 (MQ=255)                                                                                  tataACAATGTTTTGATTGCCCTTGATCTTCCTTGATAATCTGGCTAAttattacagctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaa                                                <  1:181113‑M2/129‑82 (MQ=255)                                                                                         aTGTTTTTTTTTCTCTTTAATTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgttgtattgaaaataaaaa                                         >  2:151584‑M2/1‑41 (MQ=255)                                                                                            ttttGATTGACGTTCATTTTCCTTGATAATCTGGTTAAttattactgctaaataagaccaattaaataaaaataccctttaataacaacgattaagggtttatttttgtggtatttaaaataaaaaagg                                      >  2:127773‑M2/1‑38 (MQ=255)                                                                                                gATTTCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaagaggttatttttgtggtattgaaaataaaaaagggcac                                  >  1:47101‑M2/1‑34 (MQ=255)                                                                                                 aTTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTAGTTATATGATATTTAGGAATgag                                 <  1:137261/129‑1 (MQ=255)                                                                                                    gCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaagggtcacaaaa                              <  2:132135‑M2/129‑100 (MQ=255)                                                                                                        ttGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggaacgatagggg                          <  2:56142‑M2/129‑104 (MQ=255)                                                                                                         tGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataatacaaattaaataaaaatacactttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggc                         <  1:101082‑M2/129‑105 (MQ=255)                                                                                                          gAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTa                        >  2:226763/1‑129 (MQ=255)                                                                                                               tacTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGTCCCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGAt                   <  2:210118/127‑1 (MQ=255)                                                                                                               tCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGAt                   <  1:163381/129‑1 (MQ=255)                                                                                                                             gCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCta     <  2:61199/129‑1 (MQ=255)                                                                                                                             gCTAATTATTCCTGATAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCta     <  2:174402/129‑1 (MQ=255)                                                                                                                                aattattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggtgttatttttttggtattgaaaataaaaaagggcacaaaaggggcagtatatgcaaattatcgaattt  >  1:206324‑M2/1‑2 (MQ=255)                                                                                                                                aattattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaaggggcagtatatgcaaattatcgaattt  >  1:219758‑M2/1‑2 (MQ=255)                                                                                                                                 |                                                                                                                                GGGCAAAAAAAGGGCATAATTTTGAAACAAAGG‑GCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATAT  >  USA300TCH1516_ALE/909613‑909867

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