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_ALE2,532,2980AT100.0% 86.4 / NA 28T15T (ACA→ACT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (7/21);  total (7/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGA  >  USA300TCH1516_ALE/2532165‑2532425
                                                                                                                                     |                                                                                                                               
tATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGc                                                                                                                          <  1:250801/141‑1 (MQ=255)
     gtaaaaaGTTTTAGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtttt                                                                                                                     <  2:57488/135‑1 (MQ=255)
     gTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtttt                                                                                                                     <  2:198542/141‑1 (MQ=255)
      tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATACATTCAAAAAGTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttttt                                                                                                                    <  1:26277/141‑1 (MQ=255)
      tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttttt                                                                                                                    <  1:35863/141‑1 (MQ=255)
      tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGAATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttttt                                                                                                                    >  2:276194/1‑141 (MQ=255)
        aTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAACACGAGCTTTGTATCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTca                                                                                                                  <  2:127819/141‑1 (MQ=255)
                  gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacacac                                                                                                        >  1:47483/1‑141 (MQ=255)
                               aaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATCCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCa                                                                                           <  1:287291/141‑1 (MQ=255)
                                aTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTAACATTATACACAATCAGCttttatt                                                                                          >  2:93622/1‑138 (MQ=255)
                                                      aaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTTGGATGAGTTCAATGCGTGTACTACAAAGCATTTTTCACATTACACAAAATCAGCTATTCGTTACAATCATAGAGTGGGTTTac                                                                    >  1:70241/1‑140 (MQ=255)
                                                      aaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACGTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaa                                                                    <  2:5333/141‑1 (MQ=255)
                                                       aaTTAGAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaa                                                                   <  2:215306/141‑1 (MQ=255)
                                                          aagaGTTCAATTCAGAGAGGGATGGGATAAAACGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAgg                                                                <  1:47447/138‑1 (MQ=255)
                                                                 cAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCCATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgtg                                                         <  1:127973/141‑1 (MQ=255)
                                                                 cAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgtg                                                         <  2:234389/141‑1 (MQ=255)
                                                                 aaaTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgtg                                                         <  2:122417/140‑1 (MQ=255)
                                                                  aaTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGc                                                        <  1:163635/141‑1 (MQ=255)
                                                                             ggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAggg                                             <  2:231023/141‑1 (MQ=255)
                                                                                tggcatAAACTGACCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGtt                                          <  1:215916/141‑1 (MQ=255)
                                                                                 gggctAAAATTTTCTTTGTAATGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGCGCATCTTCAAGGGGTTa                                         >  2:53949/1‑141 (MQ=255)
                                                                                    atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                      <  2:47483/141‑1 (MQ=255)
                                                                                        aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTGTTCAAATTACACACAAGCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGa                                  >  1:309241/1‑141 (MQ=255)
                                                                                           gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                               <  1:237955/141‑1 (MQ=255)
                                                                                                           aCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa               <  1:56752/141‑1 (MQ=255)
                                                                                                           aCTTCGGATGAGTAAAATGCGTTTACTACAAAGCATTTTTCACATTACAAACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa               <  2:230122/141‑1 (MQ=255)
                                                                                                                      gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTAtt    >  2:184227/1‑141 (MQ=255)
                                                                                                                        tgaaTGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGa  <  2:250862/139‑1 (MQ=255)
                                                                                                                                     |                                                                                                                               
TATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGA  >  USA300TCH1516_ALE/2532165‑2532425

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: ‑