Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 396,540 G→A 100% A208T (GCA→ACA)  efeM → putative iron uptake system component EfeM

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE396,5400GA100.0% 107.9 / NA 32A208T (GCA→ACA) efeMputative iron uptake system component EfeM
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/10);  total (22/10)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCA  >  USA300TCH1516_ALE/396411‑396677
                                                                                                                                 |                                                                                                                                         
atCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAtt                                                                                                                                >  1:730543/1‑141 (MQ=255)
     aCCAAAATTAATTCTACAAGGTTCTGTTGACCTATTAAATGAACTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATCCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGa                                                                                                                           <  1:797034/141‑1 (MQ=255)
       cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                         >  1:384069/1‑141 (MQ=255)
               aTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaaa                                                                                                                 <  1:427768/141‑1 (MQ=255)
               aTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaaa                                                                                                                 <  1:693589/141‑1 (MQ=255)
                        ggTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAAGGCGCAAGTCACACAAAAAATTTATGACTTATTTAAACCTATTTTa                                                                                                        >  1:589759/1‑141 (MQ=255)
                        ggTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATGTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTa                                                                                                        >  1:499185/1‑141 (MQ=255)
                                   ccTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                             <  1:43731/141‑1 (MQ=255)
                                           aTGAAGTTGCAACTTCTAAAATAACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAt                                                                                     <  1:426504/141‑1 (MQ=255)
                                           aTGAAATTGCAACCTCTAAAATCCCAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAt                                                                                     <  1:546738/141‑1 (MQ=255)
                                                  tGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtga                                                                              >  1:273753/1‑141 (MQ=255)
                                                      aCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTgatgat                                                                          >  1:540348/1‑141 (MQ=255)
                                                       cTTCTAAAATCACAGATGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAATTATGACGTATTTAAACCTATTTTATACACAAACGGTAAAAAATTAAGTAATGata                                                                         >  1:643077/1‑141 (MQ=255)
                                                         tCTAAAATCACAGGTGAAGAAGAAATATATGCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATc                                                                       <  1:660168/141‑1 (MQ=255)
                                                          cTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATcc                                                                      >  1:26511/1‑141 (MQ=255)
                                                              aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaag                                                                  >  1:221883/1‑140 (MQ=255)
                                                                      gTGCAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCg                                                          >  1:741547/1‑141 (MQ=255)
                                                                           aaagaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATaaa                                                     <  1:805228/140‑1 (MQ=255)
                                                                              gaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTg                                                  >  1:845522/1‑141 (MQ=255)
                                                                                  tttATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATc                                              >  1:399968/1‑141 (MQ=255)
                                                                                    tATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCaa                                            >  1:283281/1‑141 (MQ=255)
                                                                                          caTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATGATTg                                      >  1:246382/1‑141 (MQ=255)
                                                                                                    tataTGATTTTAAAGCGAACGTTGAAGGCACACAAAACAATTATTCCTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCACTTATTGGATAAAtata                            >  1:381577/1‑141 (MQ=255)
                                                                                                        tGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAGATATAAAGa                        >  1:144511/1‑141 (MQ=255)
                                                                                                        tGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATGTAAGGa                        >  1:311078/1‑141 (MQ=255)
                                                                                                              tAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaa                  <  1:661183/141‑1 (MQ=255)
                                                                                                               aaaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaac                 >  1:790163/1‑141 (MQ=255)
                                                                                                                aaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcg                >  1:429686/1‑141 (MQ=255)
                                                                                                                  gCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcggc              >  1:715864/1‑141 (MQ=255)
                                                                                                                         ttGAAGGCACACAAAAAATATATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACATCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATg       >  1:486035/1‑141 (MQ=255)
                                                                                                                          tGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGGTAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATgg      >  1:829012/1‑140 (MQ=255)
                                                                                                                              ggCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCa  <  1:133179/141‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                         
ATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCA  >  USA300TCH1516_ALE/396411‑396677

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: ‑