Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,372,751 A→T 83.9% L342* (TTA→TAA)  pbuG ← Guanine/hypoxanthine permease PbuG

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,372,7510AT83.9% 93.5 / 10.6 43L342* (TTA→TAA) pbuGGuanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand):  ref base A (5/2);  new base T (17/19);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

CTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAG  >  USA300TCH1516_ALE/2372617‑2372888
                                                                                                                                      |                                                                                                                                         
cTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGa                                                                                                                                     <  2:248379/141‑1 (MQ=255)
cTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGa                                                                                                                                     >  1:166121/1‑141 (MQ=255)
   gCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGAAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGTACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaac                                                                                                                                  >  1:357323/1‑141 (MQ=255)
   gCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTCCACCCATTAATACACCTACCACCACTAAGGCTTGTCCAGAACCTTCACTCGTTACAACACCGATTACCGTACTAAATAACACCGCTTAtcgacaac                                                                                                                                  >  2:160517/1‑134 (MQ=255)
      atGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACGTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaacaac                                                                                                                               <  1:369514/140‑1 (MQ=255)
       tGCAACTTTAAAGCTTTTTCAGTTGATCTCAGGAAAGTTTGCAGCCATTAATAACCCTATCGCCAGTAAGGCTGGTTTCGTAACTGCACTTGTTACAACAGCGATTAACGTACTAAAGAACAGCTCTTATAGGAaacaaca                                                                                                                              <  2:117727/141‑1 (MQ=255)
         cAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaacaacaac                                                                                                                            >  2:212511/1‑141 (MQ=255)
         cAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaacaacaac                                                                                                                            <  1:49333/141‑1 (MQ=255)
           aCTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCt                                                                                                                          <  1:109681/141‑1 (MQ=255)
            cttgtaaaCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCAGTAATACACCTATCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGTTTATAGGAAACAACAACCTg                                                                                                                         <  2:104686/136‑1 (MQ=255)
            cTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTg                                                                                                                         <  1:144825/141‑1 (MQ=255)
            cTTCAAAACATTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTg                                                                                                                         <  1:215285/141‑1 (MQ=255)
              tCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGtt                                                                                                                       >  1:396510/1‑141 (MQ=255)
              tCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGtt                                                                                                                       >  1:277403/1‑141 (MQ=255)
              tCAAAACCTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACGAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGtt                                                                                                                       <  1:155590/141‑1 (MQ=255)
                aaaaCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAATGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTAc                                                                                                                     <  1:331310/141‑1 (MQ=255)
                 aaaCTTTTCCAGTTTATCTCAGCAACGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATCGGAAACAACAACCTGTTACg                                                                                                                    >  2:221613/1‑141 (MQ=255)
                   aCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAACCAACAACCTGTTACGAt                                                                                                                  >  1:376998/1‑141 (MQ=255)
                            gTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCaaa                                                                                                         >  1:120578/1‑141 (MQ=255)
                              ttATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTCGCAAATc                                                                                                       >  1:287390/1‑141 (MQ=255)
                                   tcatcaAAGTTTGCAGCCATTAATACACCTACCACCACTAAGTCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACACCGCTTATCGGAAACAACAACCTGTTACGCTACTAGCAAATCCTGtt                                                                                                  <  2:306011/141‑1 (MQ=255)
                                     aGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGACACAACAACCTGTTACGATACTAGCAAATCCTGTTCt                                                                                                >  1:156114/1‑141 (MQ=255)
                                         aaacttGCTGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTATTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAAAAACAACCTGTTACGATACTACCAAATCCTGTTCTATCa                                                                                            >  2:51077/5‑141 (MQ=255)
                                          aGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCAc                                                                                           <  1:196859/141‑1 (MQ=255)
                                              tgaaGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACGTGGTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTATAGCACCTAc                                                                                       >  1:144799/4‑141 (MQ=255)
                                              tGCAGCCATTAATACACCGACCACCAATAAGGCTGGTGTCGTAACTGCACTTGTTACAACGGCGATTACCGGACTAAAGAACGGCGCTTATAGGAAACAACAACCTATTACGATACTAGCAAATCCTGTTCTAGCACCTAc                                                                                       >  1:284432/1‑141 (MQ=255)
                                                cAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCATTATCAAGCACCTAcca                                                                                     >  2:233240/1‑139 (MQ=255)
                                                                     ccaccaAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTTCCGGAGTAAAGAACAGCGCTTATAGGAAACAACAACCTGTGACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGa                                                                <  2:83212/141‑1 (MQ=255)
                                                                      cacTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGat                                                               >  1:75949/1‑141 (MQ=255)
                                                                       acTAAGGCTGGTGTCGTAACTGCACTGAGTAAAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGata                                                              <  1:12261/141‑1 (MQ=255)
                                                                        cTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGatat                                                             >  2:252417/1‑141 (MQ=255)
                                                                                  tcttgTAACTGCACTTGGTACAACAGGGATTAACGCACTAATGAACAGTGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAgttgt                                                   <  2:3152/137‑1 (MQ=255)
                                                                                    tCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGttgttg                                                 <  1:118155/141‑1 (MQ=255)
                                                                                    ccGTAAGTGCACTTGTTACAACAGCGAGTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTGGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGttgttg                                                 <  2:89751/140‑1 (MQ=255)
                                                                                       tAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAg                                              >  1:260433/1‑141 (MQ=255)
                                                                                                 tgctACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCaaa                                    <  1:84583/138‑1 (MQ=255)
                                                                                                 tGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCCAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCaaa                                    <  1:212511/141‑1 (MQ=255)
                                                                                                           gCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCt                          <  1:212111/141‑1 (MQ=255)
                                                                                                                       caaaaGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCt              <  1:104911/139‑1 (MQ=255)
                                                                                                                            gAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGAACCTACAGCAACACCTGAAGTTGATTCGATATAAGACGTTGTTGTAGTTGTTCCAAAACTTGATCCTACAATCGTAGATaaaag         >  2:331797/1‑139 (MQ=255)
                                                                                                                              aCAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATGCTACAATCGTAGCTAAAGAAt       >  1:234204/1‑141 (MQ=255)
                                                                                                                                  agcTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGATCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAACAATCTga   >  2:108310/2‑141 (MQ=255)
                                                                                                                                   gcTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGACGTTGTTGTAGTCGGTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTgac  >  2:177673/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                         
CTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAG  >  USA300TCH1516_ALE/2372617‑2372888

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑