Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,225,018 C→G 7.7% V53L (GTA→CTA)  atpA ← ATP synthase subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,225,0180CG 7.7% 153.6 / 6.1 53V53L (GTA→CTA) atpAATP synthase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (24/24);  new base G (2/2);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.14e-01

CTGGTACTTCCATGATACGACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTTGTGAGCGAAGTAATGCACTGATTTC  >  USA300TCH1516_ALE/2224880‑2225156
                                                                                                                                          |                                                                                                                                          
cTGGTACTTCCATGATACGACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTctact                                                                                                                                           <  2:314649/140‑1 (MQ=255)
   gTACTTCCATGATACGACCAGTACGTTTAACTGCGTAGCCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGc                                                                                                                                        <  2:37189/140‑1 (MQ=255)
    tactacCATGATACGACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATACCCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCt                                                                                                                                       <  2:4248/140‑1 (MQ=255)
    tACTTCCATGATACGACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCt                                                                                                                                       <  1:120986/140‑1 (MQ=255)
      cctCCATGATACGACCAGTACGTTTACCTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCa                                                                                                                                     <  1:121964/138‑1 (MQ=255)
            tGATACGACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGca                                                                                                                               >  1:299100/1‑139 (MQ=255)
            gtagatgACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAATATAACCACACCCACGTTTGACTCTTCAATGTTTTGGGCTAAACCAAGTACGCCGTTATTGAATTCTACTAGTTCACCAGcc                                                                                                                               <  2:88065/134‑1 (MQ=255)
                 cGACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAAc                                                                                                                          >  1:192014/1‑140 (MQ=255)
                      aGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCAt                                                                                                                     >  1:181727/1‑140 (MQ=255)
                       gTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCCGCCATAACGTCAtt                                                                                                                    >  2:123426/1‑140 (MQ=255)
                        tACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGATATGGAATTCTACTAGCTCACGAGCCATAACGTCAttt                                                                                                                   <  1:198165/140‑1 (MQ=255)
                         aCGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACGCCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTAGTAGCTCACCAGCCATAACGTCATTTa                                                                                                                  >  1:237035/1‑140 (MQ=255)
                         aCGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTAGTAGCTCACCAGCCATAACGTCATTTa                                                                                                                  >  1:354589/1‑140 (MQ=255)
                          cGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTaa                                                                                                                 <  1:280786/140‑1 (MQ=255)
                              tAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTACAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCAATACAGTCATTTAAtaca                                                                                                             >  2:50778/1‑137 (MQ=255)
                                    cGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCGCCCCCACGTTTGAATCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGGTATGGAATTCTACTAGCTCACCAACAAGAACGTCATTTAATACGTGAAtt                                                                                                       >  1:175662/1‑140 (MQ=255)
                                    cGTCACATTCAGTAATGCCTGTGTATGGTCCAAATATACGCACACCCACGTTTGACTCTTGAAGGTTTTGGGCTAACCCAAGTACTCCGTTATGGAATTCTACTAGCTCGCCAGCCATAACGTGATTTAATCCGTGAAtt                                                                                                       <  2:9828/140‑1 (MQ=255)
                                      tCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCCCACCTACGTTTGACTCTTCAAGGTTTTGGGCGAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTTATTTAATCCGTGAATTaa                                                                                                     <  2:266727/140‑1 (MQ=255)
                                      tCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTaa                                                                                                     >  2:111176/1‑140 (MQ=255)
                                       cACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGCCTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCTGCCATCACGTCATTTAATCCGTAAATTAAt                                                                                                    >  1:17882/1‑140 (MQ=255)
                                                    aCCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCAc                                                                                       <  1:54279/140‑1 (MQ=255)
                                                    aCCTATGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCCCCAGCCCTGCCGTCATTTACTCCGTGAATTAATGCAATACCATCAc                                                                                       >  1:241299/1‑140 (MQ=255)
                                                            aTGGTCCTAAAATAACCACCCCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGt                                                                               <  1:329022/140‑1 (MQ=255)
                                                            aTGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGt                                                                               <  2:61038/140‑1 (MQ=255)
                                                              ggTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTaa                                                                             >  1:345527/1‑140 (MQ=255)
                                                              ggTCCTAAAACAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTaa                                                                             <  2:87488/140‑1 (MQ=255)
                                                                     aaaTAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTa                                                                      >  2:13057/1‑140 (MQ=255)
                                                                      aaTAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTAc                                                                     <  2:351135/140‑1 (MQ=255)
                                                                           ccACACCCACGTTTTACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACa                                                                <  2:130106/140‑1 (MQ=255)
                                                                           ccACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACa                                                                >  2:263179/1‑140 (MQ=255)
                                                                              ccccccCGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTAGTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCa                                                             <  2:237035/138‑1 (MQ=255)
                                                                              cacCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTAGTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCa                                                             <  2:354589/140‑1 (MQ=255)
                                                                              cacCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCa                                                             >  2:78610/1‑140 (MQ=255)
                                                                                   aCGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAACACAGTACCTACATCAGTTaa                                                        >  2:354911/1‑139 (MQ=255)
                                                                                   aCGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAACACCATCACCAATTTGTAATACAGTACCTACATCCGTTAc                                                        >  1:252675/1‑140 (MQ=255)
                                                                                    cGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCCGTTACg                                                       >  2:247576/1‑140 (MQ=255)
                                                                                     gTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCCGTTACgg                                                      >  1:294675/1‑140 (MQ=255)
                                                                                      tttGACTCTTCTAGGTTTTTGGCTAAACTAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGa                                                     <  1:36396/140‑1 (MQ=255)
                                                                                        tGACCCTTCAAGGTTTTGGGCTAAACCAAGTACGTCGTTATGGAATTTTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACa                                                   <  1:116948/140‑1 (MQ=255)
                                                                                          aCTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAACACTGAACCATCACCACTTTGTAATACAGGACCTACATCAGTTACGGACAtt                                                 >  1:257925/1‑140 (MQ=255)
                                                                                                    gTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCACACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGAAATACATTACCTACATCAGCTACGCACATTTCTGACACAt                                       >  2:100564/1‑140 (MQ=255)
                                                                                                       ttGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAAt                                    <  1:235584/140‑1 (MQ=255)
                                                                                                        tGGGCTAAACCAAGTACGACGAGATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAAtt                                   >  2:77060/1‑140 (MQ=255)
                                                                                                         gggCCAAACCAAGTACGGCGTTATGGAATTCTAATAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCGTCACCAATTTGTAATACAGTACCTACATCGGTTACGGATTTTTCTGACTCATAAttt                                  <  2:77423/140‑1 (MQ=255)
                                                                                                                 ccAAGTACGTCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTtg                          <  1:285538/140‑1 (MQ=255)
                                                                                                                 ccAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTtg                          <  2:192014/140‑1 (MQ=255)
                                                                                                                     gTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTAAATTTTTGAg                      >  2:196860/1‑140 (MQ=255)
                                                                                                                     gTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACCGACATTTCTGACTCATAATTTTAAACTcgtggt                      >  2:141345/1‑138 (MQ=255)
                                                                                                                     gTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATAACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTAATAATTTTCAATTTGTGaa                      >  2:93805/1‑139 (MQ=255)
                                                                                                                      tACGCCGTTATGGAATTCTACTAGCTCACCAGACATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTTGAGAGc                     <  1:241898/140‑1 (MQ=255)
                                                                                                                        cGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTTGTGAGCGa                   >  1:344784/1‑140 (MQ=255)
                                                                                                                         tccGTTATGGAATTCTACTAGCTCACCAGCCATAACGCCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGGCAACGATAGCTCATAATCTTTTAATTGTGAGCGaa                  <  2:327375/139‑1 (MQ=255)
                                                                                                                            gTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTTGTGAGCGAAGTa               <  2:281030/140‑1 (MQ=255)
                                                                                                                                     ttCTACTAGCTCACCAGCCATACCGTCATTTAATTCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTTGTGAGCGAAGTAATGCACTGa      <  1:2047/140‑1 (MQ=255)
                                                                                                                                         actaGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTTGTGAGCGAAGTAATGCACTGATttc  <  1:308183/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                          
CTGGTACTTCCATGATACGACCAGTACGTTTAACTTCGTCACCTTCAGTAATACCTGTGTATGGTCCTAAAATAACCACACCCACGTTTGACTCTTCAAGGTTTTGGGCTAAACCAAGTACGCCGTTATGGAATTCTACTAGCTCACCAGCCATAACGTCATTTAATCCGTGAATTAATGCAATACCATCACCAATTTGTAATACAGTACCTACATCAGTTACGGACATTTCTGACTCATAATTTTCAATTTGTGAGCGAAGTAATGCACTGATTTC  >  USA300TCH1516_ALE/2224880‑2225156

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: ‑