Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 156,316 G→A 14.2% D135D (GAC→GAT)  treR_1 ← HTH‑type transcriptional regulator TreR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE156,3160GA14.2% 74.2 / 3.8 33D135D (GAC→GAT) treR_1HTH‑type transcriptional regulator TreR
Reads supporting (aligned to +/- strand):  ref base G (13/15);  new base A (3/2);  total (16/17)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

TGATATGCATTGCTATAAATCGTTTGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTGATGACATAGATACGCGAGCTAGCAATATT  >  USA300TCH1516_ALE/156179‑156448
                                                                                                                                         |                                                                                                                                    
tgatATGCATTGCTATAAATCGTTTGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTcc                                                                                                                                   <  2:137201/141‑1 (MQ=255)
 gatATGCATTGCTATAAATCGTTTGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCt                                                                                                                                  <  2:195144/141‑1 (MQ=255)
   tatGCATTGCTATAAATTTTTTGCTCAACGTATGTCTTCATGTGGTCTTCGTTTTGTGTAGTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCttt                                                                                                                                <  2:284278/141‑1 (MQ=255)
            cTATAAATCGTTTGCTCAACGCATGTATTCCTGCCGGCTTCGGTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGataa                                                                                                                       >  1:280362/1‑141 (MQ=255)
            cTATAAATCGTTTGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGataa                                                                                                                       >  1:188110/1‑141 (MQ=255)
                 aaTCGTTTGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCg                                                                                                                  >  1:250549/1‑141 (MQ=255)
                   tCGTTTGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGtt                                                                                                                <  1:263281/141‑1 (MQ=255)
                        tGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTACTCCCTTTAAATGTGCCAATGACATTTAACGGTACAAAGGTACAGCAAAATGCATCAGCTTGCTTAGAATGCTTGTCCTTTTTTTGATCATAGCGTTCCAtt                                                                                                           >  2:124547/1‑141 (MQ=255)
                             aaCGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAAt                                                                                                      <  1:121251/141‑1 (MQ=255)
                              tcGAATGTCTTCATGGCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCaacg                                                                                                     <  2:290091/140‑3 (MQ=255)
                                   tGTCTTCATGTCGTCTTCGTTTTGTGTATTCACGTTAAATGTGTCAATAACATTTAACGGTATAAAGATAAAGCAAAATGCATCACCTTGCTTAGAATGATTATCATTTTTTTAAAAATAGCGTTCCATTGCAAttcgcga                                                                                                >  2:73290/1‑135 (MQ=255)
                                      cTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTATCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGa                                                                                             >  1:247880/1‑141 (MQ=255)
                                      cTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTATCCTTTTTTTGATAATAGCGTTCAATTGCAATGACGGCAGa                                                                                             >  1:247875/1‑141 (MQ=255)
                                        tCATGTCGGCTGCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAg                                                                                           <  1:199126/141‑1 (MQ=255)
                                               gtcTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGtt                                                                                    >  1:134456/1‑141 (MQ=255)
                                                     gTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGcaaa                                                                              <  1:128659/141‑1 (MQ=255)
                                                        ttGTGTATTCACTTTAAATGTGTCAATGAAATTTAACGGTATAAAGGTAAAGTAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTGTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGcaaacaa                                                                           <  2:118867/141‑1 (MQ=255)
                                                          gtgtATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAAAAAAt                                                                         >  1:254179/1‑141 (MQ=255)
                                                               ttCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGAttt                                                                    >  2:289333/1‑141 (MQ=255)
                                                                   cTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGtat                                                                >  1:159473/1‑141 (MQ=255)
                                                                        aaTGTGTCAATGACATTTAACGGTATAAAGGTCAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTATTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACCAATGATTTGTATATTCa                                                           >  2:260459/1‑141 (MQ=255)
                                                                                      aTTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAac                                             <  1:146951/141‑1 (MQ=255)
                                                                                         tactggTATAAAGGTAAATCAAAATGAGTCCGCTTGCTTAGAATGATTGTGCTTTTTTTGATAATAGCGTTCAATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCACCACg                                          <  2:200863/137‑1 (MQ=255)
                                                                                          aaCGGTATAAAGGTCAGCCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGa                                         <  1:260782/141‑1 (MQ=255)
                                                                                              gTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCTGCAGTATGGTTTGCGACAAAACGATTTGTATATTCACTTTCTATATCTACACGAtaat                                     >  2:221510/1‑141 (MQ=255)
                                                                                                          aGCAAAATGCATCAGCTTGCTTAGAATGATTATCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTGATGACa                         <  2:247875/141‑1 (MQ=255)
                                                                                                          aGCAAAATGCATCAGCTTGCTTAGAATGATTATCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTGATGACa                         <  2:247880/141‑1 (MQ=255)
                                                                                                            cAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTACAATGACTGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTGATGACATa                       >  1:186584/1‑141 (MQ=255)
                                                                                                              aaaTGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTGATGACATAGa                     <  1:223396/141‑1 (MQ=255)
                                                                                                                aTGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGTTTTGTATATTAACTTTCTAAATAAAAACGATAATTAATTGATGACATAGATa                   >  1:221719/1‑141 (MQ=255)
                                                                                                                       aGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGTTTTGCAAACAAATGCTTTGTATATTCACTTTCTAAATCAACCCGCTATTTAATTAATGACATATATACgcgcgc            >  2:115665/1‑141 (MQ=255)
                                                                                                                                 gAATGATTGTCCTTTTTTTGATCATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTGATGACATAGATACGCGAGCTAGCAATAtt  <  1:54312/141‑1 (MQ=255)
                                                                                                                                 gAATGATTGTCCGTGTGTTTATAATAGCGTTCCATTGCAATGACGGCAGAATGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTTATGACATAGATACGCGAGCTAGCAATAtt  <  2:24431/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                    
TGATATGCATTGCTATAAATCGTTTGCTCAACGAATGTCTTCATGTCGTCTTCGTTTTGTGTATTCACTTTAAATGTGTCAATGACATTTAACGGTATAAAGGTAAAGCAAAATGCATCAGCTTGCTTAGAATGATTGTCCTTTTTTTGATAATAGCGTTCCATTGCAATGACGGCAGAAGGATGGTTTGCAAACAAATGATTTGTATATTCACTTTCTAAATCAACACGATAATTAATTGATGACATAGATACGCGAGCTAGCAATATT  >  USA300TCH1516_ALE/156179‑156448

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: ‑