Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 966,439 A→G 7.1% S169S (TCA→TCG)  addA → ATP‑dependent helicase/nuclease subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE966,4390AG 7.1% 168.6 / 4.9 56S169S (TCA→TCG) addAATP‑dependent helicase/nuclease subunit A
Reads supporting (aligned to +/- strand):  ref base A (32/20);  new base G (2/2);  total (34/22)
Fisher's exact test for biased strand distribution p-value = 6.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.71e-01

GACCCGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTATTCAACT  >  USA300TCH1516_ALE/966308‑966579
                                                                                                                                   |                                                                                                                                            
gACCCGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAga                                                                                                                                     >  1:25345/1‑140 (MQ=255)
gACCCGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGt                                                                                                                                     >  1:304125/1‑141 (MQ=255)
gACCCGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGt                                                                                                                                     >  1:72895/1‑141 (MQ=255)
gACCCGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGt                                                                                                                                     >  1:87085/1‑141 (MQ=255)
    cGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGtgatg                                                                                                                                 >  2:181653/1‑141 (MQ=255)
    cGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGtgatg                                                                                                                                 >  2:277182/1‑141 (MQ=255)
                          aGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTaa                                                                                                           <  2:79018/141‑1 (MQ=255)
                          aGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTaa                                                                                                           <  2:314815/141‑1 (MQ=255)
                              gAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACaa                                                                                                       <  1:164946/141‑1 (MQ=255)
                              gAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACaa                                                                                                       <  1:153560/141‑1 (MQ=255)
                                  atatTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCGGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGt                                                                                                   >  1:128124/1‑141 (MQ=255)
                                  atatTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCGGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGt                                                                                                   >  1:153974/1‑141 (MQ=255)
                                       ttattattaGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTc                                                                                              >  2:458522/1‑141 (MQ=255)
                                               ttttttaaCGATAGATGAGGCCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTTTCTTCATATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGt                                                                                      >  2:299550/7‑141 (MQ=255)
                                               aGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGt                                                                                      <  2:210696/141‑1 (MQ=255)
                                               aGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGt                                                                                      >  2:232945/1‑141 (MQ=255)
                                               aGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCAAATGATTATTAAACAATTGTATTTCTTTAGCGt                                                                                      >  1:145461/1‑141 (MQ=255)
                                                     aaCGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGcaaa                                                                                >  2:290429/1‑141 (MQ=255)
                                                      aCGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGcaaat                                                                               >  2:445511/1‑141 (MQ=255)
                                                         aTAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGcaaatcca                                                                            >  1:41199/1‑141 (MQ=255)
                                                                aGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTa                                                                     >  1:420753/1‑141 (MQ=255)
                                                                aGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTa                                                                     >  1:93079/1‑141 (MQ=255)
                                                                aGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTa                                                                     >  1:94782/1‑141 (MQ=255)
                                                                 ggTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTGTTGAATTAACAGAGCAATTGTCTTCAGATAGTAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATACAAATCCTaa                                                                    >  2:304697/1‑141 (MQ=255)
                                                                         aacaacATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAAttggt                                                            >  2:280394/1‑141 (MQ=255)
                                                                            aacaTTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAAttggttgg                                                         <  1:178909/141‑1 (MQ=255)
                                                                            aacaTTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAAttggttgg                                                         <  1:297950/141‑1 (MQ=255)
                                                                              caTTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGAt                                                       <  2:185612/141‑1 (MQ=255)
                                                                                ttACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCa                                                     >  2:268109/1‑141 (MQ=255)
                                                                                   cGATATCCTTGATCCTGCTTTTATTGAATTAACAGTGCAATTGTCTTCAGATAGAAGAGATGATAAGTTTCGAATACTTATTAAGCAAATGTATTTAATCAGCGTTGCAAATCCAATTCCTAAATATTGGTTGGAACagtg                                                  <  2:177594/141‑4 (MQ=255)
                                                                                   cGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAAtt                                                  <  2:177481/141‑1 (MQ=255)
                                                                                   cGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATAAAACAATTGTATGTCTTTAGCGTTGCAAAAAAAAAAAAAAAAAATTGGTTGGATCAAtt                                                  <  2:44221/141‑1 (MQ=255)
                                                                                      tatCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATTAAtattc                                               >  1:302156/1‑137 (MQ=255)
                                                                                      tatCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGAGCAGTTTCACATGATTATTAGACAAATGTATTTCTTTAGCGTTGCGAATCCAAATCCTAAAAATTGGTTGGATTAAtattc                                               >  1:43385/1‑137 (MQ=255)
                                                                                             gATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCa                                        <  2:351798/141‑1 (MQ=255)
                                                                                               tCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATa                                      <  1:36285/141‑1 (MQ=255)
                                                                                                  tGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGGTAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAATTTGGTTGGATCAATTGGTGTCACCATACga                                   >  2:365445/1‑141 (MQ=255)
                                                                                                  tGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACga                                   >  2:279573/1‑141 (MQ=255)
                                                                                                       ttATTGAATTAACAGAGCAATTGTCTTCGGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACgaagaag                              <  2:128124/141‑1 (MQ=255)
                                                                                                       ttATTGAATTAACAGAGCAATTGTCTTCGGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACgaagaag                              <  2:153974/141‑1 (MQ=255)
                                                                                                          ttGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGaagaagaag                           >  1:297204/1‑141 (MQ=255)
                                                                                                          ttGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGaagaagaag                           >  2:277478/1‑141 (MQ=255)
                                                                                                                 aaCAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCacaaca                    <  1:372078/141‑1 (MQ=255)
                                                                                                                  aCAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCAcaacaa                   >  2:152809/1‑141 (MQ=255)
                                                                                                                  aCAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCAcaacaa                   >  1:256907/1‑141 (MQ=255)
                                                                                                                  aCAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCAcaacaa                   >  1:301848/1‑141 (MQ=255)
                                                                                                                  aCAGAGCAATTGTCTTCAGATAGAAGCGATGATCAGTATCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCGTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCAcaccaa                   >  1:302103/1‑141 (MQ=255)
                                                                                                                   cAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAg                  >  2:438128/1‑141 (MQ=255)
                                                                                                                      agCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAgcgc               >  2:35194/1‑141 (MQ=255)
                                                                                                                       gCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCa              >  1:187397/1‑141 (MQ=255)
                                                                                                                         aaTTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAAc            <  1:187821/141‑1 (MQ=255)
                                                                                                                           ttGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACtt          <  1:250249/141‑1 (MQ=255)
                                                                                                                             gTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTAt        <  2:304125/141‑1 (MQ=255)
                                                                                                                             gTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTAt        <  2:72895/141‑1 (MQ=255)
                                                                                                                             gTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTAt        <  2:87085/141‑1 (MQ=255)
                                                                                                                             gTCTTCAGATAGAAGGGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTAt        <  2:25345/141‑1 (MQ=255)
                                                                                                                                   aGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTATTCAact  <  1:91441/141‑1 (MQ=255)
                                                                                                                                   aGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTATTCAact  <  1:177474/141‑1 (MQ=255)
                                                                                                                                   aGATAGAAGTGATGATCAGTTTCGAATGATTAGTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTATTCAact  <  1:92317/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                            
GACCCGAACTTTAGAACAAGCAGTGAAGCTGAAAATATTTTATTATTAGAACAAACGATAGATGAGGTCATAGAACAACATTACGATATCCTTGATCCTGCTTTTATTGAATTAACAGAGCAATTGTCTTCAGATAGAAGTGATGATCAGTTTCGAATGATTATTAAACAATTGTATTTCTTTAGCGTTGCAAATCCAAATCCTAAAAATTGGTTGGATCAATTGGTGACACCATACGAAGAAGAAGCACAACAAGCGCAACTTATTCAACT  >  USA300TCH1516_ALE/966308‑966579

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