Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 264,793 T→C 8.2% L319L (CTT→CTC)  ugpQ_2 → Glycerophosphodiester phosphodiesterase, cytoplasmic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE264,7930TC 8.2% 138.0 / 4.3 49L319L (CTT→CTC) ugpQ_2Glycerophosphodiester phosphodiesterase, cytoplasmic
Reads supporting (aligned to +/- strand):  ref base T (26/19);  new base C (2/2);  total (28/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01

ATTTATTTACGAAATTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAGCTGCTG  >  USA300TCH1516_ALE/264654‑264929
                                                                                                                                            |                                                                                                                                        
atttatttACGAAATTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTg                                                                                                                                         <  2:124026/141‑1 (MQ=255)
 tttatttaCGAAATTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGc                                                                                                                                        >  2:134014/1‑141 (MQ=255)
   tatttaCGAAATTATCATTAATCAGCGTGTTAGTCCTGCACTTAAGACAAGCGACTGTAATAGCCCAACCTGGCTTAG‑ATTTAAATGATCCAACACCGAAACGGAAGGCTAGGTTCTTTATCATTTCAATGGTGCTTGCAg                                                                                                                                      <  1:18854/141‑1 (MQ=255)
    atttaCGAAATTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGt                                                                                                                                     >  2:412138/1‑141 (MQ=255)
         cGAAATTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACAt                                                                                                                                >  1:397566/1‑141 (MQ=255)
         cGAAATTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACAt                                                                                                                                >  1:354454/1‑141 (MQ=255)
           aaaTTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGt                                                                                                                              >  1:284016/1‑141 (MQ=255)
           aaaTTATCATCAATCAGAGTGTTAGTACTGCACTTAAAACAAAAGAATGTACTCCACAAACCGGGCATAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGCTGCCTCCAGCGCCATGt                                                                                                                              >  2:437592/1‑141 (MQ=255)
            aaTTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGtt                                                                                                                             <  1:102188/141‑1 (MQ=255)
            aaTTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGtg                                                                                                                             <  1:437181/141‑2 (MQ=255)
                 tCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATc                                                                                                                        <  1:188867/141‑1 (MQ=255)
                   aTTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCgg                                                                                                                      >  2:22441/1‑141 (MQ=255)
                   aTTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCgg                                                                                                                      >  2:200560/1‑141 (MQ=255)
                         cAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACGGGAACTTAAGTCGAGTGTCTTTATAATTTCAATGGTGCTCGCAGTGACATGTTTTATCGGTTATaa                                                                                                                >  1:231044/1‑141 (MQ=255)
                         cAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTCGCAGTGACATGTTTTATCGGTTATaa                                                                                                                >  1:330664/1‑141 (MQ=255)
                               gtTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGta                                                                                                          <  1:50575/141‑1 (MQ=255)
                                ttAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGtac                                                                                                         <  2:406922/141‑1 (MQ=255)
                                            ttAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACaat                                                                                             >  2:122183/1‑141 (MQ=255)
                                                aaCAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAataata                                                                                         >  1:227467/1‑141 (MQ=255)
                                                           gTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACa                                                                              >  2:247031/1‑141 (MQ=255)
                                                                        cGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCatta                                                                 >  2:268453/1‑141 (MQ=255)
                                                                        cGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCatta                                                                 >  2:138245/1‑141 (MQ=255)
                                                                          ggCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCattatt                                                               >  2:330734/1‑141 (MQ=255)
                                                                           gCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTg                                                              >  1:212618/1‑141 (MQ=255)
                                                                                  aTTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCg                                                       <  1:363309/141‑1 (MQ=255)
                                                                                         t‑atCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGCGGTTTc                                                >  2:307026/1‑141 (MQ=255)
                                                                                                aaaCCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGAt                                          <  1:22441/141‑1 (MQ=255)
                                                                                                aaaCCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATAAAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGAt                                          <  1:200560/141‑1 (MQ=255)
                                                                                                    cGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAg                                      >  2:208776/1‑141 (MQ=255)
                                                                                                    cGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAg                                      >  2:272687/1‑141 (MQ=255)
                                                                                                       aatggAAGTCTAGGTTCTTTATAATTTCAATGGTGCTCGCAGTGACCTGTTTTATCGGTTCTCCCATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAACGGCg                                   <  2:231044/138‑1 (MQ=255)
                                                                                                       aaCGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTCGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCg                                   <  2:330664/141‑1 (MQ=255)
                                                                                                        aCGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGt                                  <  1:155541/141‑1 (MQ=255)
                                                                                                        aCGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGt                                  <  1:45181/141‑1 (MQ=255)
                                                                                                        aCGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGt                                  >  1:259277/1‑141 (MQ=255)
                                                                                                        aCGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGt                                  <  1:247973/141‑1 (MQ=255)
                                                                                                                   ggTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTa                       >  2:373904/1‑141 (MQ=255)
                                                                                                                        tttATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCg                  <  2:220084/141‑1 (MQ=255)
                                                                                                                         ttATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGt                 <  1:117616/141‑1 (MQ=255)
                                                                                                                         ttATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGt                 <  1:149914/141‑1 (MQ=255)
                                                                                                                         ttATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGt                 <  1:171981/141‑1 (MQ=255)
                                                                                                                         ttATAATTTCAATGGTGCTTGCAGTGACATGTTTTAGCGGCTATAACAGGTACGGGCTTTACAAGAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGt                 <  1:183473/141‑1 (MQ=255)
                                                                                                                               tttCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGa           <  1:134014/141‑1 (MQ=255)
                                                                                                                                  cAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAg        >  2:22771/1‑141 (MQ=255)
                                                                                                                                    aTGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAgct      >  2:358088/1‑141 (MQ=255)
                                                                                                                                    aTGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAgct      >  2:367093/1‑141 (MQ=255)
                                                                                                                                      ggTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAgctgc    >  1:143860/1‑141 (MQ=255)
                                                                                                                                        tGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAGctgctg  >  1:421695/1‑141 (MQ=255)
                                                                                                                                        tGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAGctgctg  >  1:334367/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                        
ATTTATTTACGAAATTATCATTAATCAGTGTGTTAGTACTGCACTTAAAACAAGAGAATGTATTAGACCAACCGGGCTTAGAATTTAAAT‑ATCCAAAACCGAAACGGAAGTCTAGGTTCTTTATAATTTCAATGGTGCTTGCAGTGACATGTTTTATCGGTTATAACATGTACTTACTTTACAATAATACTATCAATACAAATATCTCCATTATTGGCCATCGTGGTTTCGAAGATAAAGGCGTTGAAAATTCTATTCCGTCATTGAAAGCTGCTG  >  USA300TCH1516_ALE/264654‑264929

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑