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_ALE	396,540	0	G	A	100.0%	134.3 / NA	44	A208T (GCA→ACA)	efeM	putative iron uptake system component EfeM
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/21);  total (23/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTC  >  USA300TCH1516_ALE/396407‑396676                                                                                                                                      |                                                                                                                                         aGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACaaa                                                                                                                                    <  1:107608/140‑1 (MQ=255)   atatCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACaaaaa                                                                                                                                  <  1:477607/140‑1 (MQ=255)     atCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAt                                                                                                                                >  1:548310/1‑140 (MQ=255)       cATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTAAAGGCACACAAAAAAttt                                                                                                                              >  1:164712/1‑140 (MQ=255)         tACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTAt                                                                                                                            >  1:203477/1‑140 (MQ=255)         tACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCAAAAGACAAATTTAt                                                                                                                            >  1:241521/1‑140 (MQ=255)           ccAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGa                                                                                                                          >  1:51759/1‑140 (MQ=255)            ccaaaTGAATGTTAAACGGTTCTGTTGACCTATTAAATGAAGTTGCATCTTCTAAAATCACAAGTGAAGAAGAAATTTATTCACATTCAGATTTATATGATGTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                         <  1:192372/138‑1 (MQ=255)             aaaaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                        <  1:704830/140‑1 (MQ=255)                aTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAt                                                                                                                     >  1:279996/1‑140 (MQ=255)                   aaTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTAATCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTa                                                                                                                  >  1:408137/1‑140 (MQ=255)                     tGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaaa                                                                                                                >  1:579144/1‑140 (MQ=255)                      gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAc                                                                                                               >  1:604771/1‑140 (MQ=255)                       ttACAAGGTTCTGTTGATCTATTAAATGAAGTTGCAAATTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAcc                                                                                                              <  1:183458/140‑1 (MQ=255)                               ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                      >  1:347031/1‑140 (MQ=255)                                     tGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaa                                                                                                >  1:597983/1‑140 (MQ=255)                                       aCCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaaaa                                                                                              <  1:128028/140‑1 (MQ=255)                                             tAAATGAAGTTGCAACTTCTAAAATCACTGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaa                                                                                        >  1:484279/1‑140 (MQ=255)                                               aaTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaa                                                                                      <  1:588031/140‑1 (MQ=255)                                               aaTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAAATaaaaa                                                                                      >  1:189972/1‑140 (MQ=255)                                                aTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                     <  1:372489/140‑1 (MQ=255)                                                 ttaaGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTATAGCTAACTTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAt                                                                                    <  1:559491/138‑1 (MQ=255)                                                 tGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTCTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGTCACACAAAAATTTTTTGACTTATTAAAACCTATTTTAGAGAAaaaaaataaaaaat                                                                                    >  1:278834/1‑140 (MQ=255)                                                 tGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAACGATAAAAAAt                                                                                    >  1:411169/1‑140 (MQ=255)                                                         cAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGAGTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTCAACCTATTTTAGATAAAAAAGATAAAAAACTAAGtgat                                                                            <  1:491830/140‑1 (MQ=255)                                                         cAACTTATAAAATCATAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACTTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                            <  1:65771/140‑1 (MQ=255)                                                             ttCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAATGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGata                                                                        <  1:327712/140‑1 (MQ=255)                                                             ttCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGata                                                                        <  1:646683/140‑1 (MQ=255)                                                                               agaagaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAACAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGCTATCCAAATGAACTTCGATa                                                      >  1:579055/1‑140 (MQ=255)                                                                                     aaTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACTAAAATAAAATATGTCCTATTTAAACCGATGTTTGAGATAAAATATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGa                                                <  1:150946/140‑1 (MQ=255)                                                                                          aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAACTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCaa                                           >  1:675162/1‑140 (MQ=255)                                                                                                 tACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACAC‑AAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGa                                   <  1:98427/140‑1 (MQ=255)                                                                                                  aCAGATTTATATTATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATTACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGa                                   <  1:643269/140‑1 (MQ=255)                                                                                                   cAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGAt                                  <  1:275999/140‑1 (MQ=255)                                                                                                    aGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATa                                 <  1:252595/140‑1 (MQ=255)                                                                                                    aGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATa                                 <  1:126245/140‑1 (MQ=255)                                                                                                           tatGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAATGAGGCAATTATTAGATAAATATaa                          >  1:514568/1‑140 (MQ=255)                                                                                                              gATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGa                       <  1:578451/140‑1 (MQ=255)                                                                                                                       gCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGCTAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg              >  1:215943/1‑140 (MQ=255)                                                                                                                       gCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAGTTATCATATAAATATAAAGATAACAAcgg              >  1:205116/1‑140 (MQ=255)                                                                                                                             gTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTa        >  1:656983/1‑140 (MQ=255)                                                                                                                             gTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATAATTGGATAAATATAAAGATAACAACGGCGGTTa        >  1:586650/1‑140 (MQ=255)                                                                                                                               tGAAGGCACACAAAAAATTTATGACTTATTTAAACCTTTTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCAAAATGAACTTCTATAAAGTGAAGAAATTATTGGATAAATATAAAGATAACAACGGCGGTTATg      >  1:203217/1‑140 (MQ=255)                                                                                                                                   ggCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTc  <  1:270863/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                                         AGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTC  >  USA300TCH1516_ALE/396407‑396676

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: ‑