Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 635,184 A→T 9.5% R455S (AGA→AGT)  yhfT → putative acyl‑‑CoA ligase YhfT

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE635,1840AT 9.5% 103.3 / 4.8 42R455S (AGA→AGT) yhfTputative acyl‑‑CoA ligase YhfT
Reads supporting (aligned to +/- strand):  ref base A (20/18);  new base T (2/2);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.66e-01

AAAATGTAAAACAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTATTCCAACATTTT  >  USA300TCH1516_ALE/635051‑635308
                                                                                                                                     |                                                                                                                            
aaaaTGTAAAACAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAAt                                                                                                                       >  1:111431/1‑141 (MQ=255)
    tcgaaaaCCATCTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATGGTTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTCAATtata                                                                                                                   <  2:283773/138‑1 (MQ=255)
    tGTAAAACAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCGTGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATGGCTAGAGAAAAAATGATGTCGATGTATTGGAGAGGTGAATtata                                                                                                                   >  1:26497/1‑141 (MQ=255)
    tGTAAAACAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATtata                                                                                                                   >  1:149402/1‑141 (MQ=255)
    ggTAAAACAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATAATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTGGAAAGGTGAATtata                                                                                                                   >  2:120625/2‑141 (MQ=255)
    agTAAAACAACTATTAAAAAAGAAAGTGAATCGTTTTGAACTTCCATCGCTGATTCATCATGTAGAAAAGATGTATTTCACTGTAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATtata                                                                                                                   <  2:263208/140‑1 (MQ=255)
         aaCAATTTTTAAAAAAGAAAGTTAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATg                                                                                                              <  1:249517/141‑1 (MQ=255)
         aaCAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATg                                                                                                              <  1:249631/141‑1 (MQ=255)
         aaCAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATg                                                                                                              <  1:257191/141‑1 (MQ=255)
         aaCAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATg                                                                                                              <  1:61506/141‑1 (MQ=255)
               ttttAAAAAAGAAAGTGAAACGCTATGAAGTTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCaa                                                                                                        >  1:204688/1‑141 (MQ=255)
                      aaagaaagTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCa                                                                                                 <  2:16940/141‑1 (MQ=255)
                      aaagaaagTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCa                                                                                                 >  2:111231/1‑141 (MQ=255)
                        agaaagTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATa                                                                                               <  1:300622/141‑1 (MQ=255)
                            agTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTg                                                                                           <  1:39733/141‑1 (MQ=255)
                            agTGAAACGCTATGAAATTCCATCGATGATTCATCATGGAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTAGAATATGAATCAAGCAGCCAAAGTTg                                                                                           >  2:206260/1‑141 (MQ=255)
                             gTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTGTAATATGAATCATGCAGTCATAGTTGc                                                                                          >  1:104110/1‑141 (MQ=255)
                               gAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTATACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAg                                                                                        <  2:253549/141‑1 (MQ=255)
                               gAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAAATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGAAGCTGAGAGGTGACTTATAATCTGAATCAACCAGTCATAGTTGCAg                                                                                        >  2:311501/1‑141 (MQ=255)
                                        tGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTGAAATTCCCAGAGAAAAAATGATGTCGCGGTATTTGAAAGGTGAATTATAATATGAATCAAGCAGTGATAGTTGCGGCTAAACGaa                                                                               >  2:103300/1‑141 (MQ=255)
                                        tGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCGGCTAAACGaa                                                                               >  2:115748/1‑141 (MQ=255)
                                        tGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAACCGaa                                                                               >  2:216512/1‑141 (MQ=255)
                                        tGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGaa                                                                               >  2:216551/1‑141 (MQ=255)
                                        tGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGaa                                                                               >  1:303954/1‑141 (MQ=255)
                                              tCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCAt                                                                         >  1:64605/1‑141 (MQ=255)
                                                            atcatGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATAtggg                                                           >  1:85557/1‑140 (MQ=255)
                                                              cgtGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGTGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATAtggtgg                                                         >  1:137805/3‑141 (MQ=255)
                                                              catGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGTGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATAtggtgg                                                         >  1:137656/1‑141 (MQ=255)
                                                                         gATGTATTAAACTTCAAGTGGTAAAATTGCTAGAGAAAAAATTATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAACTATGGTGGCACTTTAATAc                                              <  2:129699/141‑1 (MQ=255)
                                                                          aTGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGGATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACa                                             >  2:16895/1‑141 (MQ=255)
                                                                           tGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTGAACGAACTGCATTTGGGAAATGTGGTGGCACTTTAAAACAt                                            >  1:266675/1‑141 (MQ=255)
                                                                               ttATACTTCAAGTGTGAAAATTGCTAGAGAAAAAATGATTTCAATGTATATGAGAGGTAAAATATAAGATTAATCAATCAGGCATAGTTGCAGCTAAACGAACTGAATTTGGGAAATATGGTGGCACTTTAAAACATTTag                                        <  2:104110/141‑1 (MQ=255)
                                                                                     tGCAAGGGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAg                                  <  2:155707/141‑1 (MQ=255)
                                                                                     cgCAAGTGGTAAAATTGCTAGAGAAAAAATGATGGCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAg                                  <  1:298948/140‑1 (MQ=255)
                                                                                      gCAATTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGGATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGTACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGa                                 <  2:250203/141‑1 (MQ=255)
                                                                                       cAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAAAATTTAGAGCCAGaa                                >  2:13023/1‑141 (MQ=255)
                                                                                                           gaAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTAtt            <  1:58461/141‑1 (MQ=255)
                                                                                                              aaaaTGATGTCGATGTATTTGAGAGGTGAATTATAATAGGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTATTCCa         <  1:90297/141‑1 (MQ=255)
                                                                                                                    atgTCGATGTATTTGAGTGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTATTCCAACAttt   <  2:137656/141‑1 (MQ=255)
                                                                                                                    atgTCGATGTATTTGAGTGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTATTCCAACAttt   <  2:137805/141‑1 (MQ=255)
                                                                                                                    atgTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTATTCCAACAttt   >  2:263554/1‑141 (MQ=255)
                                                                                                                     tgTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTATTCCAACAtttt  <  2:111431/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                            
AAAATGTAAAACAATTTTTAAAAAAGAAAGTGAAACGCTATGAAATTCCATCGATGATTCATCATGTAGAAAAGATGTATTACACTGCAAGTGGTAAAATTGCTAGAGAAAAAATGATGTCGATGTATTTGAGAGGTGAATTATAATATGAATCAAGCAGTCATAGTTGCAGCTAAACGAACTGCATTTGGGAAATATGGTGGCACTTTAAAACATTTAGAGCCAGAACAATTGCTTAAACCTTTATTCCAACATTTT  >  USA300TCH1516_ALE/635051‑635308

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: ‑