Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,004,313 G→A 8.9% H99Y (CAT→TAT)  perR ← Peroxide‑responsive repressor PerR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,004,3130GA 8.9% 111.2 / 4.2 45H99Y (CAT→TAT) perRPeroxide‑responsive repressor PerR
Reads supporting (aligned to +/- strand):  ref base G (16/25);  new base A (2/2);  total (18/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.48e-01

TTACAAACTCCATAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGCAACACTTATATTTG  >  USA300TCH1516_ALE/2004180‑2004435
                                                                                                                                     |                                                                                                                          
ttACAAACTCCATAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATg                                                                                                                            >  1:344099/1‑134 (MQ=255)
aaaCAAACTCCATAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATg                                                                                                                            <  1:436873/132‑1 (MQ=255)
  actaaCTCCATAAAGTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTCATCTTTCAAGTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGAt                                                                                                                          <  2:182927/131‑1 (MQ=255)
     cgcttcATATATTTCGATTCGATTATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAAt                                                                                                                       <  2:417183/129‑1 (MQ=255)
     aaCTCCATTAATTTCTATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAAt                                                                                                                       <  2:321765/134‑1 (MQ=255)
     aaCTCCATAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAAt                                                                                                                       <  2:62042/134‑1 (MQ=255)
       cTCCATAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGCCGAAAGCGAAAAGCAACACTCTTACCACATTGTTCACATATAAAATGATAATGa                                                                                                                     >  2:557220/1‑134 (MQ=255)
        tCCATAAATGTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGAt                                                                                                                    <  2:187033/134‑1 (MQ=255)
          cATAAATTTCCTTTTGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTa                                                                                                                  <  1:198930/134‑1 (MQ=255)
           aTAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTAt                                                                                                                 >  1:303137/1‑134 (MQ=255)
            tAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTAtg                                                                                                                >  1:483879/1‑134 (MQ=255)
                 ttCCGTTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATAATAATGATTATGTGTAt                                                                                                           <  2:240541/134‑1 (MQ=255)
                 ttCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCACCAATCTTACCACATTGTTCACATATAATATGAAAATGATTATGTGTAt                                                                                                           >  1:245099/1‑134 (MQ=255)
                 ttCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATTATTATGTGTAt                                                                                                           >  1:437636/1‑134 (MQ=255)
                    cATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTaa                                                                                                        >  2:78831/1‑134 (MQ=255)
                    cATTCGATGATGTGCTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGTTAATGATTATGTGTATTaa                                                                                                        <  2:372632/134‑1 (MQ=255)
                       tCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGt                                                                                                     >  2:543905/1‑134 (MQ=255)
                        cGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCCCATTGTTCACATATAATATGATAATGATAATGTGTATAAAAgaa                                                                                                    >  1:195608/1‑132 (MQ=255)
                                ttttACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGTATCGAc                                                                                            <  2:510242/132‑1 (MQ=255)
                                gactACATCAAATTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGAc                                                                                            <  1:77751/131‑1 (MQ=255)
                                           agtcagtcATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGtct                                                                                 <  2:374095/134‑1 (MQ=255)
                                            gtcagtcaTATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGtctc                                                                                <  2:105819/134‑1 (MQ=255)
                                             tcagtcaTATGCTGAGCTAATCTTTCAATTTCATTTACCTGTGGATATGGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTcc                                                                               <  2:429030/134‑1 (MQ=255)
                                               agtcaTATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATAATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCat                                                                             <  1:471352/134‑1 (MQ=255)
                                                   atatGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGt                                                                         <  2:181548/134‑1 (MQ=255)
                                                   ataaGCTAAACTAATTCTTCAATTTCATTTAACCGTAGATATAGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGt                                                                         <  1:452601/134‑1 (MQ=255)
                                                    tatGCTGAGCTAATCTTGCAATTTCATTTAACTGTGGATATTGAAAATCCACAATCTTACCACCTTGTTCACATATATTAGGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGtt                                                                        <  2:109600/134‑1 (MQ=255)
                                                    tatGCTGAGCTAATATTTCAATTTCATTTAACTGTTGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGtt                                                                        <  2:408023/134‑1 (MQ=255)
                                                             cTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCtttt                                                               <  2:549327/134‑1 (MQ=255)
                                                                aTCTTTCAATTTCATTTAACTGTGGAATATGAAAATCAACAATCTTACCACATTGTTCACATATAATATAATAATGATTATGTGTATTAAAGTCGAATCGACTTAATGAGTCTCCATATGTTAATTCTTTTACa                                                            >  2:44654/1‑134 (MQ=255)
                                                                 tCTTTCAATTTAATTTAACTATGGATATTGAAAATCAACAATCTTACCAAATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCAAATTGAAGAGTCTCCAAATGTTAATACTTATaaaa                                                           >  2:16192/1‑134 (MQ=255)
                                                                             aTTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATAtt                                               >  1:581514/1‑134 (MQ=255)
                                                                               ttATCTGTGAATATTTAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTa                                             <  1:193726/134‑1 (MQ=255)
                                                                               ttAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTa                                             <  2:476505/134‑1 (MQ=255)
                                                                                  agtgtgTATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAac                                          <  1:569668/132‑1 (MQ=255)
                                                                                   cTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTACTTTTTTTACAATTCCAATATCTTTAAaca                                         >  2:501951/1‑134 (MQ=255)
                                                                                   cTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAaca                                         <  2:483879/134‑1 (MQ=255)
                                                                                         atatTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCATTAAAAACTATTa                                   >  1:127012/1‑134 (MQ=255)
                                                                                          tatTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTTCATATGTTAATTCTTTTACACTTCCATTATCTTTAAACACTCTTaa                                  >  2:457339/1‑134 (MQ=255)
                                                                                          tatTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTTCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTaa                                  >  2:395285/1‑134 (MQ=255)
                                                                                                            ttACCACATTTTTCACATATAATATGATAATGATTATGTGTATTTATCATGTTTCTACTTTATGTGCCTCCATATCTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGc                <  2:271428/134‑1 (MQ=255)
                                                                                                               ccACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGCAac             >  1:388394/1‑134 (MQ=255)
                                                                                                                  gaTTGGTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGCAACACt          <  2:552149/133‑1 (MQ=255)
                                                                                                                    ttGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGCAACACTta        <  2:344099/134‑1 (MQ=255)
                                                                                                                         cacaTATAATATAATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGCAACACTTATAttt   >  1:583691/1‑134 (MQ=255)
                                                                                                                          acaTATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACACTTCCAATATCTTTAAACACTCTTCAGTTATTATATATTATCGCAACACTTATATTTg  >  2:134316/1‑134 (MQ=255)
                                                                                                                          acaTATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGCAACACTTATATTTg  <  1:393177/134‑1 (MQ=255)
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TTACAAACTCCATAAATTTCCATTCGATGATGTGTTACGTCAAAGTCAGTCATATGCTGAGCTAATCTTTCAATTTCATTTAACTGTGGATATTGAAAATCAACAATCTTACCACATTGTTCACATATAATATGATAATGATTATGTGTATTAAAGTCGAATCGACTTGATGAGTCTCCATATGTTAATTCTTTTACAATTCCAATATCTTTAAACACTCTTAAGTTATTATATATTGTCGCAACACTTATATTTG  >  USA300TCH1516_ALE/2004180‑2004435

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: ‑