Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,391,192 Δ1 bp 7.4% coding (427/1461 nt) alsT → Amino‑acid carrier protein AlsT

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,391,1920C. 7.4% 155.0 / 9.3 54coding (427/1461 nt)alsTAmino‑acid carrier protein AlsT
Reads supporting (aligned to +/- strand):  ref base C (28/21);  new base . (2/2);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

GCGATTGTTTTAGGCGGTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCA  >  USA300TCH1516_ALE/1391054‑1391325
                                                                                                                                          |                                                                                                                                     
gCGATTGTTTTAGGCGGTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCa                                                                                                                                     <  1:237832/141‑1 (MQ=255)
 cGATTGTTTTAGGCGGTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAg                                                                                                                                    >  2:10780/1‑141 (MQ=255)
  gATTGTTTTAGGCGGTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATCAAGATGGTGGATTCCGTGGTGGTCCAGc                                                                                                                                   >  2:245433/1‑141 (MQ=255)
  gATTGTTTTAGGCGGTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGc                                                                                                                                   <  1:556035/141‑1 (MQ=255)
   aTTGTTTTAGGCGGTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCt                                                                                                                                  >  2:679176/1‑141 (MQ=255)
           aGGCGGACCAGGAGCAGTATTTTGGCTGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTGTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGCGGTGGTCCAGGTTACTctat                                                                                                                          >  2:513610/1‑141 (MQ=255)
             ggagTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTa                                                                                                                        <  2:725882/138‑1 (MQ=255)
                 tCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATGAAGTACATGATAAAGTTGGTGGATTCCTTGGTGGGCCAGCTTACtgtaggacgaa                                                                                                                    >  1:378802/1‑134 (MQ=255)
                 tCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTaa                                                                                                                    <  1:339858/141‑1 (MQ=255)
                 tCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTaa                                                                                                                    <  1:339828/141‑1 (MQ=255)
                     ggTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTCAAgcg                                                                                                                >  1:391751/1‑139 (MQ=255)
                           gTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAAt                                                                                                          >  1:265131/1‑141 (MQ=255)
                                     tgtgGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGT‑CAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCt                                                                                               >  1:753000/1‑141 (MQ=255)
                                     tgtgGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGT‑CAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCt                                                                                               >  1:753062/1‑141 (MQ=255)
                                      gtgGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCt                                                                                               <  2:374800/141‑1 (MQ=255)
                                       ggggTTATTGCCTTTATAGGTGCAGCGAGGGCATTTAGAGAAGCGCCTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGTTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTa                                                                                              <  1:132159/140‑1 (MQ=255)
                                               tGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGt                                                                                      >  1:49905/1‑141 (MQ=255)
                                                   tttATAGGTGCAGTGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTAttt                                                                                  <  1:639764/141‑1 (MQ=255)
                                                           tGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAATTGGCTAGGTATCGTATTTGCGAtttt                                                                          >  2:269824/1‑141 (MQ=255)
                                                           tGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTTCCGTATTTGCGAtttt                                                                          >  2:393684/1‑141 (MQ=255)
                                                           tGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGAtttt                                                                          >  2:56517/1‑141 (MQ=255)
                                                            gCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTa                                                                         <  1:676975/141‑1 (MQ=255)
                                                              atggAGTGCCTTTATAGAAGCGACTTTGGCACAGGTATATAAAATCCCTACGCCAGGCACTTCATATCGCGATAGTACTGCTTCATATTTTACTAAAAGTAAAAAACAAAAATGGCTAGGTATCGTATTTGCGATTTTaat                                                                       <  2:803536/138‑1 (MQ=255)
                                                               gCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTaatt                                                                      >  2:794926/1‑141 (MQ=255)
                                                                cGATTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATAGTATTTGCGATTTTaatta                                                                     >  2:737139/1‑141 (MQ=255)
                                                                cGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTaatta                                                                     >  1:729466/1‑141 (MQ=255)
                                                                   gTGCATTTATAGAAGCGTCGTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTTGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTaattacaa                                                                  <  2:169319/141‑1 (MQ=255)
                                                                   gTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTaattacaa                                                                  >  2:639719/1‑141 (MQ=255)
                                                                   gTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTaattacaa                                                                  >  1:391358/1‑141 (MQ=255)
                                                                    tGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTaattacaat                                                                 <  1:110484/141‑1 (MQ=255)
                                                                      cATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTaattacaatta                                                               >  2:511550/1‑141 (MQ=255)
                                                                      cATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTGGCGCTTTTaattacaatta                                                               >  2:29087/1‑141 (MQ=255)
                                                                                aGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTAcatttgcatt                                                     >  1:80484/1‑141 (MQ=255)
                                                                                aGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTAcatttgcatt                                                     >  2:683000/1‑141 (MQ=255)
                                                                                aGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTAcatttgcatt                                                     >  1:754250/1‑141 (MQ=255)
                                                                                       ttGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATGTTAATTACAATTACATTTGCCTTTGTAttt                                              >  1:220286/1‑141 (MQ=255)
                                                                                        tGGCTCAAGTCTATAAAGTACATGATAAAGATGGTGGATTCAGCAGTGGTCCAAATTTCTAGTTTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTa                                             >  2:590941/1‑141 (MQ=255)
                                                                                         ggCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTaa                                            >  2:738180/1‑141 (MQ=255)
                                                                                            tCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAacac                                         <  1:676465/141‑1 (MQ=255)
                                                                                             cAGGTTTAGAAAGTACTTGATAAAGGTGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAGTAATGGCTAGGTATCGTATTTGCGATTTTAATTACTATTACATTTGCATTTGTATTTAAcaca                                        <  2:134770/141‑1 (MQ=255)
                                                                                                 tttATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGc                                    <  2:244871/141‑1 (MQ=255)
                                                                                                 tttATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGc                                    <  1:10475/141‑1 (MQ=255)
                                                                                                   tataAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCaa                                  <  2:178264/141‑1 (MQ=255)
                                                                                                    ataAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAAt                                 >  1:267281/1‑141 (MQ=255)
                                                                                                       aaGTACATGATAAAGATGGTGGATTCCGTGGTGGT‑CAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTaa                             <  2:753000/141‑1 (MQ=255)
                                                                                                       aaGTACATGATAAAGATGGTGGATTCCGTGGTGGT‑CAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTaa                             <  2:753062/141‑1 (MQ=255)
                                                                                                                        ggtggATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCg             <  2:635576/141‑1 (MQ=255)
                                                                                                                        ggtggATTCCGGGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCg             <  1:181516/141‑1 (MQ=255)
                                                                                                                         gtggATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGt            <  1:794926/141‑1 (MQ=255)
                                                                                                                          tggATTCCGTGGTTGGCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGtt           <  1:10780/141‑1 (MQ=255)
                                                                                                                          tggATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATGTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGACGtt           >  1:257153/1‑141 (MQ=255)
                                                                                                                           ggATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTa          <  2:391358/141‑1 (MQ=255)
                                                                                                                            gATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTaa         >  1:781329/1‑141 (MQ=255)
                                                                                                                                   tggtggTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCa  >  1:225084/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                     
GCGATTGTTTTAGGCGGTCCAGGTGCAGTATTTTGGATGTGGGTTATTGCATTTATAGGTGCAGCGAGTGCATTTATAGAAGCGACTTTGGCTCAGGTTTATAAAGTACATGATAAAGATGGTGGATTCCGTGGTGGTCCAGCTTACTATATTACTAAAGGTTTAAATCAAAAATGGCTAGGTATCGTATTTGCGATTTTAATTACAATTACATTTGCATTTGTATTTAACACAGTGCAATCTAATACAATTGCGGAGTCGTTAAATACGCA  >  USA300TCH1516_ALE/1391054‑1391325

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: ‑