Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	396,540	G→A	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_ALE	396,540	0	G	A	100.0%	152.3 / NA	46	A208T (GCA→ACA)	efeM	putative iron uptake system component EfeM
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/17);  total (29/17)

GATACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGT  >  USA300TCH1516_ALE/396399‑396675                                                                                                                                              |                                                                                                                                         gATACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACaaa                                                                                                                                    <  1:561290/148‑1 (MQ=255)         aGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTAt                                                                                                                            >  1:797575/1‑148 (MQ=255)            tatCACACCAAAATTAATGTTACAATGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAATAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                         <  1:977513/148‑1 (MQ=255)                aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAt                                                                                                                     <  1:1232265/148‑1 (MQ=255)                    cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaa                                                                                                                 >  1:835186/1‑148 (MQ=255)                    cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGACTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaa                                                                                                                 >  1:287925/1‑148 (MQ=255)                               ttACAAGGTTCTGTTGACCTATGAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                      <  1:1227221/148‑1 (MQ=255)                                 aCAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCAATTTTagaa                                                                                                    >  1:942836/1‑147 (MQ=255)                                   aaGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACCCAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaa                                                                                                  >  1:1035861/1‑148 (MQ=255)                                   aaGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATACACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaa                                                                                                  >  1:755808/1‑148 (MQ=255)                                    aGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACACAAAATTTATGACTTATTTAAACCTATTTTAGAGaaa                                                                                                 >  1:151135/1‑148 (MQ=255)                                       ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaaag                                                                                              >  1:313474/1‑147 (MQ=255)                                       ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTGATGACTTATTTAAACCTATTTTAGAGaaaaaa                                                                                              >  1:578505/1‑148 (MQ=255)                                        tCTGTTGACCAATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAg                                                                                             <  1:22878/148‑1 (MQ=255)                                             tGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaa                                                                                        <  1:1127881/148‑1 (MQ=255)                                              gACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaa                                                                                       >  1:960752/1‑148 (MQ=255)                                              gACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaa                                                                                       >  1:1092141/1‑148 (MQ=255)                                                ccTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                     <  1:1025363/148‑1 (MQ=255)                                                   aTTAAAGGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGCAGTTGTCATTCAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTa                                                                                  >  1:913870/1‑148 (MQ=255)                                                        aTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGGATCGTAAATATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtga                                                                             >  1:1236176/1‑148 (MQ=255)                                                        aTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtga                                                                             >  1:334050/1‑148 (MQ=255)                                                         tGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                            >  1:890179/1‑148 (MQ=255)                                                                   aCTTCTAAAATCACAGGTGAAGAAGAAATTTCTTCACATCCAGATTTATATGATTTTAAAGCGACCGTTGAAGGCACACAACAAATTTATGACTTCTTTACACCTCTTTTAGAGACGAAAGATAAAAACTTAAGTGATGAGATCCcaa                                                                  >  1:824434/1‑148 (MQ=255)                                                                         aaaaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACt                                                            >  1:731262/1‑148 (MQ=255)                                                                            aTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGCTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCg                                                         >  1:237754/1‑148 (MQ=255)                                                                                   gTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGt                                                  <  1:443607/148‑1 (MQ=255)                                                                                   gTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGt                                                  <  1:200796/148‑1 (MQ=255)                                                                                           gaaATCTATTCACATAAAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑Aat                                         <  1:955433/148‑1 (MQ=255)                                                                                               tttATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATGTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑Aattatt                                     <  1:1238703/148‑1 (MQ=255)                                                                                                   ttCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGAt                                 <  1:1061112/148‑1 (MQ=255)                                                                                                    tCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGGCTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGCACTACGATAAAGTGAATC‑AATTAGTGtata                                >  1:465807/1‑148 (MQ=255)                                                                                                       caTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAGGTGAATC‑AATAATTGGATAAat                             >  1:232909/1‑148 (MQ=255)                                                                                                                ttATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAACGATAAAGAATTAAGTGGTGATATCCAAATGAACTACGATAAAGTGAATC‑AATTATTGGATAACTATAAAGATa                    >  1:268942/1‑148 (MQ=255)                                                                                                                  atatGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATaac                  <  1:155631/148‑1 (MQ=255)                                                                                                                     tGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAG‑AATTCTAATTATTGGATAAATATAAAGATaacaac               <  1:300859/148‑1 (MQ=255)                                                                                                                      gATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAAcg              >  1:233108/1‑148 (MQ=255)                                                                                                                        ttttAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAAcggc            >  1:1191788/1‑148 (MQ=255)                                                                                                                         tttAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAAcggcg           <  1:479131/148‑1 (MQ=255)                                                                                                                         tttAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAAcggcg           <  1:381758/148‑1 (MQ=255)                                                                                                                           tAAAGCGAACGTTGAAGGCACACAAAAAATCTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGt         <  1:537342/148‑1 (MQ=255)                                                                                                                            aaaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGtt        >  1:517390/1‑148 (MQ=255)                                                                                                                            aaaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGtt        >  1:343356/1‑148 (MQ=255)                                                                                                                             aaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGTTa       >  1:347675/1‑148 (MQ=255)                                                                                                                              aGCGAACGTTGAAGGCACACAACAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGTTAt      >  1:632308/1‑148 (MQ=255)                                                                                                                                  aaCGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGACAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAgc  >  1:1244343/1‑147 (MQ=255)                                                                                                                                  aaCGTTGAAGGCACACAAAAAATTTACGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGt  >  1:816971/1‑148 (MQ=255)                                                                                                                                              |                                                                                                                                         GATACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATC‑AATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGT  >  USA300TCH1516_ALE/396399‑396675

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: ‑