Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 175,610 T→A 13.3% H61Q (CAT→CAA)  ywqE_1 → Tyrosine‑protein phosphatase YwqE

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE175,6100TA13.3% 75.0 / 5.3 30H61Q (CAT→CAA) ywqE_1Tyrosine‑protein phosphatase YwqE
Reads supporting (aligned to +/- strand):  ref base T (10/16);  new base A (2/2);  total (12/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.48e-01

TCCGACAAATGAAACAGAGATGATGGATCTTTTAAAACAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATATTGATCGAAAAGTTATTAACGGTATTAATGATTCACGCTATTTACTAATA  >  USA300TCH1516_ALE/175472‑175748
                                                                                                                                          |                                                                                                                                          
tCCGACAAATGAAACAGAGATGATGGATCTTTTAAAACAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCatat                                                                                                                                          >  1:169573/1‑141 (MQ=255)
        agaaaaCAGAGAAGAGCGATCTTTTAAAACAAGCGACAACACAACGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTAAAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCt                                                                                                                                  <  2:223881/138‑1 (MQ=255)
           aaaCAGAGATGATGGATCTTTTAAAACAAGCGACAAAACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAATGAAATCATGTATAAACCATATTGAAAGCtaaa                                                                                                                               >  2:17901/1‑138 (MQ=255)
             aCAGAGATGATGGATCTTTTAAAACAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTagag                                                                                                                             <  1:222519/141‑1 (MQ=255)
             aCAGAGATGATGGATCTTTTAAAACAAGCGACAACACAAGCTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATCGAAAGCTTagag                                                                                                                             <  1:200668/141‑1 (MQ=255)
              cAGATATGATGCACCTTTTAAAACAAGCGACAACACAAGGTGTTACAGAAATCATTGTACCATCACATCACTTACACCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAgg                                                                                                                            <  2:146810/141‑1 (MQ=255)
               agagATGATGGATCTTTTAAAACAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGa                                                                                                                           >  1:227598/1‑141 (MQ=255)
                               ttAAAACAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCATAGAGGCAGTACAAGCCCTACAt                                                                                                           >  1:58266/1‑141 (MQ=255)
                                 aaaaCAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCt                                                                                                         <  1:48151/141‑1 (MQ=255)
                                    aCAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTaaa                                                                                                      >  2:201007/1‑141 (MQ=255)
                                      aaGCGACAACACAAGGCGTCACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGt                                                                                                    <  2:114059/141‑1 (MQ=255)
                                               cacaATGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATg                                                                                           <  2:280332/141‑1 (MQ=255)
                                                  aaGTTGTTACAGCAATCATTGTAACATCACATCACGTACAACCTCGGTATACCACACCGAGAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCTCGGAATCTAAAGTTTTATTATGGTc                                                                                        <  2:60593/141‑1 (MQ=255)
                                                   aGGTGTTACAGAAATCCTTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTAAGAGGAAGTACAAGCACTAACTCTAAAGTATTATTACCGTCa                                                                                       >  1:55693/1‑141 (MQ=255)
                                                         caCAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACATCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGCAAAt                                                                                 <  2:172705/140‑1 (MQ=255)
                                                                 tCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCAAATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTa                                                                         >  1:98044/1‑141 (MQ=255)
                                                                 tCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCAAATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTa                                                                         >  1:98071/1‑141 (MQ=255)
                                                                            ccacatcacTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATc                                                              <  1:7565/140‑1 (MQ=255)
                                                                               catcacTTACCTCCTCGATATACCACACCTATAGAAAAAGTGAAAGTATGGTTAAACCATATTGAAAGCTTAGAGGAAGTACAACAACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAAGTACCGATCAAATCCtt                                                           <  2:81627/141‑1 (MQ=255)
                                                                                atcacTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTa                                                          >  1:24409/1‑141 (MQ=255)
                                                                                    cTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTGTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGa                                                      <  2:152050/141‑1 (MQ=255)
                                                                                       aCATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCAAATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGatat                                                   <  2:98071/141‑1 (MQ=255)
                                                                                       aCATCCTCGATATACCACAACTATAGAAAAAGTGAAATCATGTTTAAACCAAATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGatat                                                   <  2:98044/141‑1 (MQ=255)
                                                                                                      cacaCCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATATTGATCGAAAAGttat                                    <  1:103928/141‑1 (MQ=255)
                                                                                                              taGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGCGGTCTAAGCACTAAATAAAGAAATTTAGCAAGGTCAGGAAATAGGAAGTACCGATGAGAGCAAGAAGGATATTGATCTAAAAGTTATTAACGGTa                            >  1:207843/1‑141 (MQ=255)
                                                                                                                 aaaaaGTGAAATTATGTTTGCACCATAGTGATAGCTTAGAGGAAGTACAAGCACGAAACCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCTAATCCTTAATGATATTGATCGAAAAGTTATTAACGGTATTa                         <  2:123249/141‑1 (MQ=255)
                                                                                                                             cATCTTGAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATCTTGATCGAAACGTTATTAACGGTATTAATGATTCACGCt             >  2:73562/1‑141 (MQ=255)
                                                                                                                                    aaaCCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATATTGATCGAAAAGTTATTAACGGTATTAATGATTCACGCTATTTACt      <  1:201007/141‑1 (MQ=255)
                                                                                                                                       ccATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATATTGATCGAAAAGTTATTAACGGTATTAATGATTCACGCTATTTACTAAt   <  2:169573/141‑1 (MQ=255)
                                                                                                                                       ccATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATATTGATCGAAAAGTTATTAACGGTATTAATGATTCACGCTATTTACTAAt   >  2:237359/1‑141 (MQ=255)
                                                                                                                                        cATATTGAAAGCTTAAAGGAAGTACGAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATATTGATCGAAAAGTTATTAACGGTATTAATGATTCACGCTATTTACTAATa  >  1:142699/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                          
TCCGACAAATGAAACAGAGATGATGGATCTTTTAAAACAAGCGACAACACAAGGTGTTACAGAAATCATTGTAACATCACATCACTTACATCCTCGATATACCACACCTATAGAAAAAGTGAAATCATGTTTAAACCATATTGAAAGCTTAGAGGAAGTACAAGCACTAAATCTAAAGTTTTATTATGGTCAGGAAATAAGAATTACCGATCAAATCCTTAATGATATTGATCGAAAAGTTATTAACGGTATTAATGATTCACGCTATTTACTAATA  >  USA300TCH1516_ALE/175472‑175748

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: ‑