Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 888,887 A→G 7.6% D137G (GAT→GGT)  nfnB → Nitroreductase NfnB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE888,8870AG 7.6% 142.1 / 2.1 52D137G (GAT→GGT) nfnBNitroreductase NfnB
Reads supporting (aligned to +/- strand):  ref base A (19/29);  new base G (2/2);  total (21/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

TATTTTAAAAACAGATCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACATTATATTAATATGTATAA  >  USA300TCH1516_ALE/888750‑889026
                                                                                                                                         |                                                                                                                                           
tATTTTAAAAACAGATCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATc                                                                                                                                           <  1:541044/140‑1 (MQ=255)
        aaaCAGATCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGTGACATGTTGGAAATCGCCATTATATATCTATGAGTCTAAAGTa                                                                                                                                   >  2:248500/1‑140 (MQ=255)
           cAGATCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGa                                                                                                                                >  2:216140/1‑140 (MQ=255)
           cAGATCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGa                                                                                                                                >  2:430383/1‑140 (MQ=255)
            aGATCTAAGACAACGTCAAAATCATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGaa                                                                                                                               <  2:662430/140‑1 (MQ=255)
            aGATCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGaa                                                                                                                               <  2:519380/140‑1 (MQ=255)
              aTCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAGGaaaa                                                                                                                             >  2:70224/1‑140 (MQ=255)
                 cgaGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAAGCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAaca                                                                                                                          <  2:760856/138‑1 (MQ=255)
                   aGACAACGTCACAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACt                                                                                                                        <  1:217281/140‑1 (MQ=255)
                        aCGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATc                                                                                                                                           >  2:419860/1‑116 (MQ=255)
                        aCGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATc                                                                                                                                           <  1:419860/116‑1 (MQ=255)
                             aaaaTGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATaaag                                                                                                              <  1:475366/140‑1 (MQ=255)
                             aaaaTCATGAGTACTAGTTTGCATTTGGTGCAGATGCACAAAATCTTATGTGGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATaaag                                                                                                              <  2:759890/140‑1 (MQ=255)
                              aaaTGATGAAAACTCCTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATaaaga                                                                                                             <  1:423200/140‑1 (MQ=255)
                                atgatgAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATaaagaaa                                                                                                           >  2:307268/1‑140 (MQ=255)
                                agcatgaATACGTCTTTGAATTTGGTGAATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATaaagaaa                                                                                                           <  2:78359/137‑1 (MQ=255)
                                    tgaAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTATTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATg                                                                                                       >  1:399990/1‑140 (MQ=255)
                                     gaAATCTACTGTGGTTTGGGGGCATATGGACAAAATCTTATGTGGCTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGa                                                                                                      <  2:398642/140‑1 (MQ=255)
                                              tttGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGc                                                                                             <  1:486408/140‑1 (MQ=255)
                                              tttGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGc                                                                                             <  1:674684/140‑1 (MQ=255)
                                                tGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTg                                                                                           >  1:379426/1‑140 (MQ=255)
                                                 gCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGGTCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGCTGAAGTTCTTGCTgg                                                                                          >  1:737326/1‑140 (MQ=255)
                                                 gCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGGTCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTgg                                                                                          >  2:623943/1‑140 (MQ=255)
                                                      tGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCt                                                                                     <  1:308980/140‑1 (MQ=255)
                                                       ggTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCtt                                                                                    >  2:486660/1‑140 (MQ=255)
                                                           cATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGAATAGATGTAGATGAAGTTCTTGCTGGATTCTTatat                                                                                >  1:139628/1‑140 (MQ=255)
                                                           cATATGCACAAAATCTTATGGTGTTACTTTACGAAGCGGGACTAGGTACATGTTGGAAATCGCCAGTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTatat                                                                                <  1:248500/140‑1 (MQ=255)
                                                             tatGCAAAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGAGCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATAttt                                                                              <  2:141355/140‑1 (MQ=255)
                                                                gCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGACCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAAc                                                                           <  1:332244/140‑1 (MQ=255)
                                                                       aTCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTa                                                                    <  1:145570/140‑1 (MQ=255)
                                                                        tCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAg                                                                   <  2:514326/140‑1 (MQ=255)
                                                                        tCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAg                                                                   >  2:35553/1‑140 (MQ=255)
                                                                           tATGTTGTTACTTTATGAAGCGGGAATAGGTACATGAACGTAACCGCCATTATATATCTATGATCCTACAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAg                                                                <  1:389886/140‑1 (MQ=255)
                                                                            aTGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAgg                                                               <  2:433680/140‑1 (MQ=255)
                                                                                       ttATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCCTGCTGGATTCTTATATTTAACGGATTTAAAAGGAGATACGCCTa                                                    >  2:39489/1‑140 (MQ=255)
                                                                                       ttATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACAATTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGGTATGCATa                                                    >  2:37737/1‑140 (MQ=255)
                                                                                       ttATGAAGCCGGAATAGGTACATGGTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTa                                                    <  2:468090/140‑1 (MQ=255)
                                                                                               cGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGcacca                                            <  1:215988/140‑1 (MQ=255)
                                                                                                    aTAGTTACATGTTGGAAATCGCTATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTaa                                       <  1:151994/140‑1 (MQ=255)
                                                                                                       ggTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTaaaaa                                    >  1:19754/1‑140 (MQ=255)
                                                                                                             ttggagAAAACGCCATTATACATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAACAATAGaaa                              <  2:16622/135‑1 (MQ=255)
                                                                                                              gtgggAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAAc                             <  1:747236/137‑1 (MQ=255)
                                                                                                                   aaaTCGCCATTATATATCTATGGTCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAAt                        <  1:623943/140‑1 (MQ=255)
                                                                                                                   aaaTCGACATTATATATATATGGTTGTTAAGTAAGAAAATTATTTGATATAAATAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAAt                        <  2:737326/140‑1 (MQ=255)
                                                                                                                    aaTCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAAtt                       <  1:619575/140‑1 (MQ=255)
                                                                                                                     aTCTCCATTATATATCTAAGATCGTAAAGTAAGAAAAATACTTAGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTa                      <  2:314633/140‑1 (MQ=255)
                                                                                                                        gCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGCGATATGCCTAAACCACAATGTACAAATAGAAACTTAAATACAt                   >  2:316481/1‑140 (MQ=255)
                                                                                                                        gCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTACCAGTAGAAACATAATTACAt                   >  2:362862/1‑140 (MQ=255)
                                                                                                                         ccATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACAtt                  <  1:177131/140‑1 (MQ=255)
                                                                                                                            ttATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACATtata               >  2:152991/1‑140 (MQ=255)
                                                                                                                                   tCTATGATCCTAAAGTAAGACAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAATATAGAAACTTAATTACATTATCTTAatat        >  2:226065/1‑140 (MQ=255)
                                                                                                                                        gATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTAGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACATTATATTAAtatatata   >  2:28101/1‑140 (MQ=255)
                                                                                                                                         aTCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACATTATATTACTATGTATaa  >  2:488069/1‑140 (MQ=255)
                                                                                                                                         aTCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACATTATATTAATATGTATaa  >  1:546209/1‑140 (MQ=255)
                                                                                                                                         aTCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACATTATATTAATATGTATaa  <  1:35553/140‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                           
TATTTTAAAAACAGATCCAAGACAACGTCAAAATGATGAAAACTACTTTGCATTTGGTGCATATGCACAAAATCTTATGTTGTTACTTTATGAAGCGGGAATAGGTACATGTTGGAAATCGCCATTATATATCTATGATCCTAAAGTAAGAAAAACACTTGGTATAAAGAAAGATGAAGTTCTTGCTGGATTCTTATATTTAACGGATTTAGAAGGAGATATGCCTAAAGCACCACGTAAAAATAGAAACTTAATTACATTATATTAATATGTATAA  >  USA300TCH1516_ALE/888750‑889026

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: