Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,532,298	A→T	100%	T15T (ACA→ACT)	femA_3 →	Aminoacyltransferase FemA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,532,298	0	A	T	100.0%	124.1 / NA	44	T15T (ACA→ACT)	femA_3	Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (19/25);  total (19/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAT  >  USA300TCH1516_ALE/2532168‑2532416                                                                                                                                   |                                                                                                                       ttccaaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTactaca                                                                                                                     <  2:293407/130‑1 (MQ=255)  tatAATCATTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTActacaa                                                                                                                    <  1:534293/132‑1 (MQ=255)     aaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGc                                                                                                                 <  1:77521/134‑1 (MQ=255)         aGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGCGTTCAATGCGTTTACTACAAAGCAttt                                                                                                             >  2:148175/1‑134 (MQ=255)            ttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTAAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACATTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTc                                                                                                          >  2:140415/1‑134 (MQ=255)              ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcac                                                                                                        <  1:352801/134‑1 (MQ=255)               tGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcaca                                                                                                       >  2:385355/1‑134 (MQ=255)                gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGAATACTACAAAGCATTTTTCACAt                                                                                                      >  2:607348/1‑134 (MQ=255)                 ataaaataaaAAAATAGCATTATTAATAAATTCAAAAATTATAGTCCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAtt                                                                                                     >  1:92515/1‑134 (MQ=255)                      ataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCGATGCGTTTACTACAAAGCATTTTTTACAATacaca                                                                                                >  1:565137/1‑134 (MQ=255)                          aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAAt                                                                                            <  1:229897/134‑1 (MQ=255)                                  cATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAtt                                                                                    >  1:485669/1‑134 (MQ=255)                                    ttattaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAAAGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCGCATTACACACAATCAGCTATTCa                                                                                  >  1:312585/1‑134 (MQ=255)                                       ttaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTa                                                                               <  2:43618/134‑1 (MQ=255)                                           taaATTCAAAAATTGTAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGAGTTTACTACAAAGCATTTTTAACATTACACACAATCAGCTATTCATTACAAt                                                                           >  2:601048/1‑134 (MQ=255)                                            aaaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATc                                                                          <  2:140042/134‑1 (MQ=255)                                                tCAATAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCCCTGCGTCTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATag                                                                      <  2:458428/134‑1 (MQ=255)                                                  aaataTTATAGTTCAATTCAGAGATGGATGGTATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAAGGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATagag                                                                    <  1:112633/134‑1 (MQ=255)                                                   aaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                   >  2:502190/1‑134 (MQ=255)                                                      aTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGa                                                                <  1:459840/134‑1 (MQ=255)                                                       ttATGGTTCAATTCAGAGATGGATGGGATAAAATGATCTTTGTAACGTTGACTTCGGTTGAGTTCAATGCTTTTACTACAAATCATGTTTCACATTACACACAATCTGCTATTCATTACAATCATAGAGTTGAt                                                               <  2:65483/134‑1 (MQ=255)                                                         ataGTTCAATTTATAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAttt                                                             <  2:390376/134‑1 (MQ=255)                                                           aGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAACCACAGAGTTGATTTaa                                                           >  2:231609/1‑134 (MQ=255)                                                            gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGCGTCCAATGCGCTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGATATGATTCaaa                                                          >  2:245104/1‑134 (MQ=255)                                                             ttCAATTCAGAGAGGGATGGGATAATATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaaa                                                         <  1:405476/134‑1 (MQ=255)                                                                     agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCCGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgt                                                 >  2:322133/1‑134 (MQ=255)                                                                     agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgt                                                 >  1:587450/1‑134 (MQ=255)                                                                          gagatgggatAAAATGAACTTTGTAACGGTGACTTCGGAAGAGTCAAAAGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATc                                            <  1:266586/132‑1 (MQ=255)                                                                           ggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                           <  2:533166/134‑1 (MQ=255)                                                                              tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGt                                        <  2:455828/134‑1 (MQ=255)                                                                               ggcaaaaaaTGAACTTTGTAATGGGGACTTCGCATGGGTTCAATGCCTTTACTGCGAAGCATTTTTCACAATACACACAATCAGCTATTCATTACAATCATAGAGTTAATTTAAAAGTCGATGTGCATCTTGTa                                       <  2:604895/129‑1 (MQ=255)                                                                                 gatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATATTGTAgg                                     >  1:40083/1‑134 (MQ=255)                                                                                         gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATCGAGTTGATTTAAAAAGCGATGTGCATAATGTAGGGGTTAAAg                             >  1:213771/1‑134 (MQ=255)                                                                                                gTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                      <  1:385355/134‑1 (MQ=255)                                                                                                   aCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTTACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGCTGACAATgt                   >  2:459859/1‑133 (MQ=255)                                                                                                   aCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGCGTTGATTTAAAAGGCGATGTGCATCTAGTAGGGGTTAAAGATGACaaagg                   >  1:546869/1‑131 (MQ=255)                                                                                                      ttGACCTCGCCTGAGTTCAATGCGTTTACTACACAGCATGCATCACAACACAGTGGCGCAGCTATTCAGTCCAAGCAGAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCa                <  1:196390/134‑1 (MQ=255)                                                                                                          cTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAAGGGTCAAGTg            >  2:538061/1‑134 (MQ=255)                                                                                                           ttCGGATTAGTTCAATGCGTTTACTACGAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGa           <  1:65326/134‑1 (MQ=255)                                                                                                             cgaaTGAGTTCAATTCGTTTACTAAAAAGCATATTACACATAACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAtt         <  1:329909/131‑1 (MQ=255)                                                                                                                aTGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa      <  2:240214/134‑1 (MQ=255)                                                                                                                aTGAGTTCAATGCGTGTACTACAAAGCCTTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa      <  2:110326/134‑1 (MQ=255)                                                                                                                 tGAGTTTAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAg     <  1:529200/134‑1 (MQ=255)                                                                                                                  gattgcAATGCGTTTAATACAAAGCATGTTTCAGATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAgg    <  2:422794/129‑1 (MQ=255)                                                                                                                  gAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCACCTTGGAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAgg    <  1:25024/134‑1 (MQ=255)                                                                                                                    tttCAATGCGTTTACTACTAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAt  <  2:60714/133‑1 (MQ=255)                                                                                                                                   |                                                                                                                       TTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAT  >  USA300TCH1516_ALE/2532168‑2532416

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: ‑