Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	130,854	(T)5→1	9.9%	intergenic (‑94/+272)	sarS ← / ← yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 130853	55 (0.880)	6 (0.100)	6/256	NT	9.9%	intergenic (‑93/+276)	sarS/yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA
	?	USA300TCH1516_ALE	130858 =	55 (0.880)					intergenic (‑98/+271)	sarS/yfhA	HTH‑type transcriptional regulator SarS/putative siderophore transport system permease protein YfhA

TAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAGTATTA  >  USA300TCH1516_ALE/130724‑130997                                                                                                                                       |                                                                                                                                            attataaaatctctaattttgtcatggtcattatatttcattgttttatctccttgtatatgcactttattttaatataacacaatataataagaaaaataatccataatttacaattaaaaataatatgatatATTaaa                                                                                                                                        <  2:640533‑M2/6‑1 (MQ=255)   tataaaatctccaattttgtcatggttattatatttcattgtattatctccttgtatatgcactttattttaatataacacaatataataatcaaaataatacttaatgtaaaattaaaaataatatgttatATTCAAAt                                                                                                                                      >  2:131092‑M2/133‑140 (MQ=255)    aaTCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAAtt                                                                                                                                     <  1:534454/140‑1 (MQ=255)        tctAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTAGTAAAATTtgtg                                                                                                                                 >  2:629589/1‑140 (MQ=255)            aTTTTGTCATTGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                             <  1:184869/140‑1 (MQ=255)            aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                             <  1:635295/140‑1 (MQ=255)            aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                             <  2:606692/140‑1 (MQ=255)            aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                             <  1:306796/140‑1 (MQ=255)            aTTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGtttt                                                                                                                             <  2:214299/140‑1 (MQ=255)                 gTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAAt                                                                                                                        <  1:339080/140‑1 (MQ=255)                  tCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATACTTTACGATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATa                                                                                                                       >  1:719057/1‑140 (MQ=255)                   cacggTTATGATATTTCATTGTTTTTTCTCCTTGTATATGCACTTTATTTTAATATGATATATTATAATATGAAAAATAATCTATAATTTAAAATGAACAATTATATGATATTTTTATTAAAATTCTTATTTTTtaataa                                                                                                                      >  2:177143/4‑140 (MQ=255)                        ttattaTATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGAc                                                                                                                 <  2:92927/140‑1 (MQ=255)                        ttattaTATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGAc                                                                                                                 <  1:215272/140‑1 (MQ=255)                            tataTTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTa                                                                                                             <  2:28237/140‑1 (MQ=255)                            tataTTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTa                                                                                                             <  2:29601/140‑1 (MQ=255)                              tatTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATc                                                                                                           <  1:597666/140‑1 (MQ=255)                              tatTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATc                                                                                                           <  1:597814/140‑1 (MQ=255)                                  tatttcattattttatctccttgtatatgcactttattttaatataacacaatataataagaaaaataatccataatttacaattaaaaataatatgatatATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAac                                                                                                       <  2:540039‑M2/39‑1 (MQ=255)                                     ttGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACt                                                                                                    <  1:260681/140‑1 (MQ=255)                                      tGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACta                                                                                                   >  1:709436/1‑140 (MQ=255)                                      tGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACAAAATATAATAAGAGAAATAATCCATAATTTACAGTTAAAAATAATATGATATTTTTATTAACATTTGTGTCTTTGAATAAATGACATTATCAAACACtc                                                                                                   >  1:17964/1‑139 (MQ=255)                                        ttttATCTCCTTTTATATGCGCTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACtata                                                                                                 <  2:25627/140‑1 (MQ=255)                                           gttttatctccttgtatatgcactttattttaatataacacaatataataagaaaaataatccataatttacaattaaaaataatatgatatATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATAttt                                                                                              >  1:75600‑M2/93‑140 (MQ=255)                                             tctcCTTGTATATGCACTTTATTTTAATATCACATTATCTAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTaa                                                                                            >  2:54224/1‑140 (MQ=255)                                              ctcCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTaaa                                                                                           >  1:252718/1‑140 (MQ=255)                                                 cTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGACTAAATGACATTATCAAACACTATATTTAAATaa                                                                                        >  1:260022/1‑140 (MQ=255)                                                    ttataTGCACTTTCTTTTAATATAACACAATATAATAGTAAAAATAATCCATAAGTTACAATTAAAAATAATATGATATTTTTACAACAATTTGTGTTTTTTAATAAATGACATTATCAAACACTATATTTAAATAAGaa                                                                                     <  2:744800/139‑1 (MQ=255)                                                    atataTGCACTTTAGTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGaa                                                                                     <  1:568976/139‑1 (MQ=255)                                                       tatGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATa                                                                                  <  2:623540/140‑1 (MQ=255)                                                          atatgcactttattttaatataacacaatataataagaaaaataatccataatttacaattaaaaataatatgatatATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGtt                                                                               >  2:119955‑M2/78‑140 (MQ=255)                                                              tttATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAGTATTATATTTTTATTAAAATTTGTGTTTTTGCATAAATGACCTTATCATCCACGCTATTTAACTACGAAATACTtctct                                                                           >  1:651975/1‑139 (MQ=255)                                                               ttATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATATATGACAGAACCAAACACTATATTTATATAGGAAATAGTTATGGa                                                                          >  1:140243/1‑140 (MQ=255)                                                                  ttttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGatat                                                                       >  1:733444/1‑140 (MQ=255)                                                                   tttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATAtt                                                                      >  2:278783/1‑140 (MQ=255)                                                                   tttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATAtt                                                                      <  1:762950/140‑1 (MQ=255)                                                                    ttAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATAttt                                                                     >  1:533997/1‑140 (MQ=255)                                                                       atatAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGaa                                                                  <  2:57701/140‑1 (MQ=255)                                                                       atatAACAAAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGaa                                                                  <  2:395207/140‑1 (MQ=255)                                                                         ataACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGaaaa                                                                <  2:26138/140‑1 (MQ=255)                                                                            acacAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATc                                                             >  2:400854/1‑140 (MQ=255)                                                                            acacAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATc                                                             >  2:748396/1‑140 (MQ=255)                                                                            acacAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATc                                                             >  1:546604/1‑140 (MQ=255)                                                                                   ataataataAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGTTATTTGAAAAATCGAAGAat                                                      <  2:320199/140‑1 (MQ=255)                                                                                   ataataAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAat                                                      <  2:191073/140‑1 (MQ=255)                                                                                   agaataaGAAAAATAATTCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAat                                                      <  2:168932/138‑1 (MQ=255)                                                                                     aataaGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTGTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAatat                                                    <  1:68066/140‑1 (MQ=255)                                                                                      ataaGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTACAATTTGTGTTTTTGAATAAATGCCATTTGCGAACACTATATTTCAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAAtttt                                                   >  1:175663/1‑140 (MQ=255)                                                                                      ataaGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATatt                                                   >  1:364722/1‑140 (MQ=255)                                                                                           aaaaaTAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATattgattg                                              <  1:6546/140‑1 (MQ=255)                                                                                           aaaaaTAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATattgattg                                              >  1:179888/1‑140 (MQ=255)                                                                                            aaaaTAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATAGAAGAATAttgattga                                             >  2:115671/1‑140 (MQ=255)                                                                                                taatCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGAtatt                                         <  2:733444/140‑1 (MQ=255)                                                                                                   tCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTAAAAAATCGAAGAATATTGATTGACATtata                                      >  1:715161/1‑140 (MQ=255)                                                                                                    ccATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAg                                     >  1:662748/1‑140 (MQ=255)                                                                                                          ataatttacaattaaaaataatatgatatATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATg                               <  2:354933‑M2/111‑1 (MQ=255)                                                                                                              cAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTc                           >  1:747640/1‑140 (MQ=255)                                                                                                                 ttAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGgt                        <  2:443239/140‑1 (MQ=255)                                                                                                                 ttAAAAATAATATCAAATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGgt                        <  1:751928/140‑1 (MQ=255)                                                                                                                  tAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGgtg                       <  2:8893/140‑1 (MQ=255)                                                                                                                          atatGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATCTTTGAAAAATCGAAGACTCTAGATCGTTATAAGAGAATATGAGTCGGTGTTATTTGt               >  1:477334/1‑140 (MQ=255)                                                                                                                                  tttttATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAg       <  2:130988/140‑1 (MQ=255)                                                                                                                                      tATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAGTAtt   >  1:29979‑M2/2‑140 (MQ=255)                                                                                                                                       attaAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAGTATTa  >  1:334877/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                            TAAAATCTCTAATTTTGTCATGGTTATTATATTTCATTGTTTTATCTCCTTGTATATGCACTTTATTTTAATATAACACAATATAATAAGAAAAATAATCCATAATTTACAATTAAAAATAATATGATATTTTTATTAAAATTTGTGTTTTTGAATAAATGACATTATCAAACACTATATTTAAATAAGAAATAGTTATCGATATTTGAAAAATCGAAGAATATTGATTGATATTATAGAATATGAGTCGGTGTTATTTGTATATAAAGTATTA  >  USA300TCH1516_ALE/130724‑130997

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.