Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 536,758 C→T 100% P202L (CCA→CTA)  rplY → 50S ribosomal protein L25

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE536,7580CT100.0% 175.8 / ‑6.5 57P202L (CCA→CTA) rplY50S ribosomal protein L25
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (23/33);  total (23/34)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGCTGATGTTAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACCAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGCATGGTGCTTTTTGTGTTA  >  USA300TCH1516_ALE/536621‑536892
                                                                                                                                         |                                                                                                                                      
tGCTGATGTTAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTGTTGAAGGCGAACAACAAACTGAAGAACTAGa                                                                                                                                     <  2:66940/141‑1 (MQ=255)
 gCTGATGTTAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGaa                                                                                                                                    >  2:245255/1‑141 (MQ=255)
 gCTGATGTTAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGaa                                                                                                                                    >  2:324043/1‑141 (MQ=255)
  tggATGTTAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAg                                                                                                                                   <  1:150090/139‑1 (MQ=255)
      tGTTAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAgttgt                                                                                                                               >  1:281897/1‑141 (MQ=255)
        ttAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGttgttg                                                                                                                             <  1:299840/141‑1 (MQ=255)
          aacgTAACTGGCTACTTAAAACTCGAACGCGCTTGAGCTGAAGCAGTAGTAACAGTATTTGCTACAATTGAAGAACCAACTGAAGACGAAATCTAAGTTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGc                                                                                                                           <  2:167766/138‑1 (MQ=255)
             gTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGaa                                                                                                                        <  1:304080/141‑1 (MQ=255)
                aCTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGc                                                                                                                     >  1:324473/1‑141 (MQ=255)
                  tGGCTACTACAAAATCGAAAACTTCTCAGCTCACTCAGTAGTCACAGTAGTTCCTCAAACTGAAGAACCAACTGAAGAAGATATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCaa                                                                                                                   <  2:220958/141‑1 (MQ=255)
                  tGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCaa                                                                                                                   <  1:334269/141‑1 (MQ=255)
                    gCGACTTCAAAATCGAAAACGATTCTGCTGAATCAGTAGTTACAGTAGTTGCTCCAACTGAAGAACCAAATGACGAAGAAAGGGAAACGAAGGAAGACGACCANCAAACTGAAGAGCTAGAAGTTGTTGGCGAAGGCAaag                                                                                                                 >  2:1125/1‑141 (MQ=255)
                    gCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCaacg                                                                                                                 >  2:113793/1‑139 (MQ=255)
                      gACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAaagaa                                                                                                               >  2:283673/1‑141 (MQ=255)
                          tCAAAATCTAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACg                                                                                                           <  2:392765/141‑1 (MQ=255)
                          tCAAAAGCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGGAAAGAAGACg                                                                                                           <  2:267285/141‑1 (MQ=255)
                                               cTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAATACTGAAGAGTAAt                                                                                      <  1:332203/141‑1 (MQ=255)
                                               cTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAAt                                                                                      <  1:366249/141‑1 (MQ=255)
                                                tGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAAtt                                                                                     <  1:194908/141‑1 (MQ=255)
                                                agAAGCAGTAGGAACAGTAGTCGCTCCAACTGAAGAACCAACTGAAGAACCAACACGACCAACGAGAGACTATCAACGAACTGAACAACTAGAAGTTTGTGGAGATTGCAATGGAGACAAAGATTATTCTGATGAGTAAtt                                                                                     <  2:102322/140‑1 (MQ=255)
                                                 gAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAAttt                                                                                    >  1:320110/1‑141 (MQ=255)
                                                  aaTCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGGAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAAtttt                                                                                   <  1:182474/141‑1 (MQ=255)
                                                    tCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTaa                                                                                 <  2:45388/141‑1 (MQ=255)
                                                        tagtaACAGGAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTg                                                                             <  2:36026/141‑1 (MQ=255)
                                                         agtaACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGt                                                                            >  1:161832/1‑141 (MQ=255)
                                                         agtaACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGt                                                                            <  2:2846/141‑1 (MQ=255)
                                                          ataACAGTAGTTTCCCCAACTGAAGAACCAACTGAAGAAGAAATCTAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGtt                                                                           <  2:360101/140‑1 (MQ=255)
                                                           taACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTa                                                                          >  1:96339/1‑141 (MQ=255)
                                                           taACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTa                                                                          >  1:131347/1‑141 (MQ=255)
                                                           taACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTa                                                                          >  1:357376/1‑141 (MQ=255)
                                                              cAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACAt                                                                       <  1:245255/141‑1 (MQ=255)
                                                              cAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACAt                                                                       <  1:324043/141‑1 (MQ=255)
                                                                   gtTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAATAATTATAATCTGTTACATTAAAg                                                                  >  1:367414/1‑141 (MQ=255)
                                                                     tGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTaaattg                                                                >  2:373023/1‑138 (MQ=255)
                                                                     tGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGtt                                                                >  2:312543/1‑141 (MQ=255)
                                                                     tGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGtt                                                                >  1:291936/1‑141 (MQ=255)
                                                                        cacaactgaagaaccaaatacataaAAATGCTAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAAGCTGTTACATTAAAGttttt                                                             <  2:377361/139‑1 (MQ=255)
                                                                        accaactgaagaaccaaccgaagaaGAAATCGAAGCTATGGAAGGAGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGttttt                                                             <  2:282025/140‑1 (MQ=255)
                                                                         ccaaatgaagaaccaactgaagaaGAAATAGAAGCTANGGAAGGACAACAATAAACTGTAGAACTAGAAGTTGTTGGCTAAAGCAAAAAAAAAAAAAAAAAAACTGACGAGTAATTTTAATCTGTTACATTAAAGTTTTta                                                            <  2:261242/141‑1 (MQ=255)
                                                                                 agaaccaactgaagaaGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGt                                                    >  2:125850/1‑141 (MQ=255)
                                                                                 agaaccaactgaagaaGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGATTCTCTACTTTGt                                                    >  2:351795/1‑141 (MQ=255)
                                                                                      caactgaagaaGAAATCGAAGCGATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAAc                                               <  1:1125/141‑1 (MQ=255)
                                                                                        actcaagaaTAAATCGAATCTGTAGGTGATGAACAACAAACGTAAGAACTAGAAGTTTTTGGCAAAAGCAAAGAAGTCGAAGAAAAATCTTAAGAGTAATTTTAATCTATTACATTTAATTTTTTATACTTTGTTTAACaa                                             <  2:276300/141‑1 (MQ=255)
                                                                                         ctgaagaaGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAg                                            <  1:283673/141‑1 (MQ=255)
                                                                                                     tCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGAACTGTGCTTAt                                >  2:122723/1‑141 (MQ=255)
                                                                                                        aaGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTAtttt                             >  1:314495/1‑141 (MQ=255)
                                                                                                        aaGCTATGGAAGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTAtttt                             >  1:152199/1‑141 (MQ=255)
                                                                                                           cTAGGGAAGGGGAACAACAAAATGAACAACCAGGTGTTGCGGGCGATAGGGAAGAATACGAAGAAAAAACTGAAGAGTAATTTTAATCTTTTACAGCAAAGGTTTTATACTTTGTTTAACAACCACTGTGCTTATTTTAat                          <  2:179368/141‑1 (MQ=255)
                                                                                                                 aaGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGc                    <  1:6167/141‑1 (MQ=255)
                                                                                                                 aaGGCGAACAACAAACTGAAGAACTAGAAGATGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGc                    <  1:130503/141‑1 (MQ=255)
                                                                                                                  aGGCGAACAACAAGCTGAAGCACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGCa                   <  1:325417/141‑1 (MQ=255)
                                                                                                                  aGGCGAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGCa                   <  1:153249/141‑1 (MQ=255)
                                                                                                                      gAACAACAAACTGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGCCGAAAAAAAAACTGAAGAGTAATTTTAATCTGTTACATTGAAGTTTTTATACTTTGTTTAACAAGCACACTACTTGTTTGAAGATAAGCATGGt               >  1:106276/1‑141 (MQ=255)
                                                                                                                                 tGAAGAACTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGCATGGTGCTTTTTgtgt    <  2:60246/141‑1 (MQ=255)
                                                                                                                                 ggaaaaaCTAAAAGTTTGTGGCGAAAGCAAAAAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACCTTGTTCAACAAGCACTTTGCTTATTTTAATATAAGCATGGTTCTTTTTgtgt    <  2:113679/140‑1 (MQ=255)
                                                                                                                                  gaagaaCTAGAAGTTGTTGGCGAAAGCCAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGCATGGTGCTTTTTGTGtt   <  1:325552/141‑1 (MQ=255)
                                                                                                                                   aagaaCTAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGCATGGTGCTTTTTGTGtta  >  1:373529/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                      
TGCTGATGTTAAAGTAACTGGCGACTTCAAAATCGAAAACGATTCAGCTGAATCAGTAGTAACAGTAGTTGCTCCAACTGAAGAACCAACTGAAGAAGAAATCGAAGCTATGGAAGGCGAACAACAAACTGAAGAACCAGAAGTTGTTGGCGAAAGCAAAGAAGACGAAGAAAAAACTGAAGAGTAATTTTAATCTGTTACATTAAAGTTTTTATACTTTGTTTAACAAGCACTGTGCTTATTTTAATATAAGCATGGTGCTTTTTGTGTTA  >  USA300TCH1516_ALE/536621‑536892

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: ‑