Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 19,009 C→T 18.2% S222F (TCC→TTC)  gdpP → Cyclic‑di‑AMP phosphodiesterase GdpP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE19,0090CT18.2% 100.2 / 16.8 44S222F (TCC→TTC) gdpPCyclic‑di‑AMP phosphodiesterase GdpP
Reads supporting (aligned to +/- strand):  ref base C (18/18);  new base T (2/6);  total (20/24)
Fisher's exact test for biased strand distribution p-value = 2.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

ACATTATTTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTGAA  >  USA300TCH1516_ALE/18873‑19145
                                                                                                                                        |                                                                                                                                        
aCATTATTTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGAt                                                                                                                                      <  2:238924/141‑1 (MQ=255)
   ttattTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCaa                                                                                                                                   >  2:83915/1‑141 (MQ=255)
    tattTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAAt                                                                                                                                  >  2:160185/1‑141 (MQ=255)
    tattTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAAt                                                                                                                                  >  1:276137/1‑141 (MQ=255)
        tttAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGt                                                                                                                              >  2:163251/1‑141 (MQ=255)
                    cGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTaaa                                                                                                                  <  2:145640/141‑1 (MQ=255)
                     gATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAAt                                                                                                                 <  1:419076/141‑1 (MQ=255)
                     gATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAAt                                                                                                                 <  1:234853/141‑1 (MQ=255)
                             tACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAat                                                                                                         <  2:298875/141‑1 (MQ=255)
                                gCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATAtt                                                                                                      >  2:77053/1‑141 (MQ=255)
                                       atgaatgaTACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGAc                                                                                               <  1:557318/141‑1 (MQ=255)
                                           atgaTACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTag                                                                                           >  1:190477/1‑141 (MQ=255)
                                            tgaTACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTaga                                                                                          <  2:80677/141‑1 (MQ=255)
                                              aTACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTagaag                                                                                        <  1:661304/141‑1 (MQ=255)
                                                aCGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAgaagaa                                                                                      <  1:128002/141‑1 (MQ=255)
                                                 cGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAAt                                                                                     <  2:189449/141‑1 (MQ=255)
                                                   cAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCt                                                                                   <  2:141780/141‑1 (MQ=255)
                                                        ttCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAAtt                                                                              <  1:333416/141‑1 (MQ=255)
                                                            ggaaTCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGat                                                                          <  2:44297/139‑1 (MQ=255)
                                                            gAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGat                                                                          <  1:445297/141‑1 (MQ=255)
                                                                tCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCt                                                                      <  2:107375/141‑1 (MQ=255)
                                                                    cTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACATTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAg                                                                  <  1:783902/141‑1 (MQ=255)
                                                                    cTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAg                                                                  <  1:783984/141‑1 (MQ=255)
                                                                      cAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTc                                                                >  2:54435/1‑141 (MQ=255)
                                                                              aCGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGt                                                        >  1:9880/1‑141 (MQ=255)
                                                                                gcgTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGa                                                      >  1:83059/1‑141 (MQ=255)
                                                                                  gtgtCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGaaa                                                    <  2:171218/141‑1 (MQ=255)
                                                                                    gtCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGaaaaa                                                  >  2:100278/1‑141 (MQ=255)
                                                                                        ttAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACGGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAgtg                                              >  2:254858/1‑141 (MQ=255)
                                                                                                tGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTAt                                      >  1:350835/1‑141 (MQ=255)
                                                                                                 gggCAACTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATc                                     >  1:39417/1‑141 (MQ=255)
                                                                                                     aaCTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGc                                 <  1:784452/141‑1 (MQ=255)
                                                                                                     aaCTGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGc                                 <  1:784367/141‑1 (MQ=255)
                                                                                                        tGAGTATAATATATTTTTCAAAAGATACAGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTNAAAAAAGTGTTGGTTATCGTGCCCa                              <  1:241930/141‑1 (MQ=255)
                                                                                                             ataataTATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTaa                         >  1:212761/1‑141 (MQ=255)
                                                                                                               aataTATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACa                       >  1:348720/1‑141 (MQ=255)
                                                                                                                atatatTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACAt                      >  2:306437/1‑141 (MQ=255)
                                                                                                                       tttCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTAt               <  1:327782/141‑1 (MQ=255)
                                                                                                                         tCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCg             >  1:629307/1‑141 (MQ=255)
                                                                                                                          cAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCgg            <  2:29016/141‑1 (MQ=255)
                                                                                                                           aaaaGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGgt           >  2:263309/1‑141 (MQ=255)
                                                                                                                            aaaGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGgtg          >  2:130563/1‑141 (MQ=255)
                                                                                                                                   cAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTGa   >  2:107101/1‑141 (MQ=255)
                                                                                                                                    aGTTTCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTGaa  <  1:132348/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                        
ACATTATTTTTAGATAACTACGATGAGATTACGCAAAATATGAATGATACGCAGCGTTCGGAAATCAACTCAATGGTAACGCGTGTCATTAGTCGATGGGCAACTGAGTATAATATATTTTTCAAAAGATACAGTTCCGATCAATTCGTAGCCTATTTAAATCAAAAAATATTAGCTGACTTAGAAGAATCTAAATTTGATATCTTGAGTCAATTACGTGAAAAAAGTGTTGGTTATCGTGCCCAATTAACATTAAGTATCGGTGTTGGTGAA  >  USA300TCH1516_ALE/18873‑19145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑