Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,038,244 T→A 7.2% T39S (ACA→TCA)  USA300HOU_RS10295 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,038,2440TA 7.2% 151.5 / 2.9 55T39S (ACA→TCA) USA300HOU_RS10295hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (16/35);  new base A (2/2);  total (18/37)
Fisher's exact test for biased strand distribution p-value = 5.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

TATATTAAACATAGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAACCCTCCCGATCATGACAT  >  USA300TCH1516_ALE/2038104‑2038382
                                                                                                                                            |                                                                                                                                          
tataTTAAACATAGGTTTGCTATATTTGCTAAAGAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCtgt                                                                                                                                            >  1:337801/1‑141 (MQ=255)
 atatTAAATATAGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATTAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCtgtg                                                                                                                                           <  1:335652/141‑1 (MQ=255)
   atTAAACACAGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGac                                                                                                                                         <  2:31397/141‑1 (MQ=255)
       aaCATAGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCt                                                                                                                                     <  1:117000/141‑1 (MQ=255)
       aaCATAGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCt                                                                                                                                     <  1:468480/141‑1 (MQ=255)
        aCATAGGTTTGCTATCTTTTTGAAATCAAAGAAATAATGCTCGATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGAGGATATTTTGATCGACAACCGCTGTGACACCTa                                                                                                                                    <  1:667556/141‑1 (MQ=255)
            aGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATTTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTTACGc                                                                                                                                <  1:473357/141‑1 (MQ=255)
            aGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGAGACACCTCACGc                                                                                                                                >  1:498845/1‑141 (MQ=255)
            aGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGAGACACCTAACGc                                                                                                                                >  1:394576/1‑141 (MQ=255)
               tttACTATCTTTTTTAAATAAAACAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCa                                                                                                                             <  1:79488/141‑1 (MQ=255)
                  tcTATCTTTTTTAAATAAAAGAAATAATGCTCCATGGATACGTTCATGTTAAATCAATAAAATGATGAATCCAGCTAACCCATATACATGTTGGATGATGATATTTTGATCGACAACCGCTGTGCCACCTAACGCCCACtt                                                                                                                          <  2:68853/140‑1 (MQ=255)
                  gCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACtt                                                                                                                          <  2:370092/141‑1 (MQ=255)
                  gCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACtt                                                                                                                          >  1:414720/1‑141 (MQ=255)
                     aTCTTTTTTAAATAAAAGAAATAATACTCTATGGGTAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCCAACACCCACTtata                                                                                                                       >  1:580062/1‑141 (MQ=255)
                      acTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATAc                                                                                                                      <  1:74996/140‑1 (MQ=255)
                      aatttttaAAAAAAAAAAAATAATGCTCTAAGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATAc                                                                                                                      <  2:349637/139‑1 (MQ=255)
                       cTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACg                                                                                                                     <  1:119264/141‑1 (MQ=255)
                        ttttttAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGt                                                                                                                    >  1:532434/1‑141 (MQ=255)
                              aaataaaAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGtaaataa                                                                                                              <  2:52508/141‑1 (MQ=255)
                                  aaaaGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATc                                                                                                          <  2:35604/141‑1 (MQ=255)
                                      gAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGa                                                                                                      <  2:12370/141‑1 (MQ=255)
                                       aaaTAAAGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGaa                                                                                                     <  1:24316/141‑1 (MQ=255)
                                        aataatGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAAtacggaat                                                                                                    >  2:68124/1‑134 (MQ=255)
                                            atGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACg                                                                                                <  1:213333/141‑1 (MQ=255)
                                            atGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACg                                                                                                <  1:373811/141‑1 (MQ=255)
                                             ttgtctAGGGGTAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCCCTGTGACACCTAACGCCCACTTAAACGTAAGTAAAATCACGACTAAcac                                                                                               >  2:609689/4‑139 (MQ=255)
                                                tctATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAAt                                                                                            <  1:354175/141‑1 (MQ=255)
                                                 ctATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACACTTGCGATGAGAAAATCACGAATAACGCAATa                                                                                           <  1:686663/141‑1 (MQ=255)
                                                    tGGATAAGATCAAATAAAAACAAAAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACa                                                                                        <  1:392938/141‑1 (MQ=255)
                                                     ggATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTCACACCTAACGCCCACTTATACGTAAATGAAATCACGAATAACGCAATACCaa                                                                                       >  2:537329/1‑141 (MQ=255)
                                                             tCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGAGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAg                                                                               <  2:394576/141‑1 (MQ=255)
                                                             tCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGAGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAg                                                                               <  2:498845/141‑1 (MQ=255)
                                                                  tAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAGATAAAATCACGAATAACGCACTAACAAGTTGCAAGataaa                                                                          >  2:563789/1‑140 (MQ=255)
                                                                  tAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGataat                                                                          >  2:37565/1‑141 (MQ=255)
                                                                      aTCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAAc                                                                      <  2:486269/141‑1 (MQ=255)
                                                                      aTCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGAGATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAAc                                                                      <  1:244765/141‑1 (MQ=255)
                                                                          ataaaataaTGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTCAATAAGATCACGGATAACGCAATAACAAGTTGCAAGATAATAAACCTTc                                                                  >  1:470713/1‑141 (MQ=255)
                                                                            aaaataaTGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATACAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAAccaccgc                                                                >  2:222195/1‑136 (MQ=255)
                                                                            aaaataaTGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGc                                                                <  2:259607/141‑1 (MQ=255)
                                                                                taatCAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCACTAACAAGTTGCAAGATAATAAACCTTCGCAttt                                                            >  1:472241/1‑141 (MQ=255)
                                                                                    gAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGaaa                                                        >  1:80479/1‑141 (MQ=255)
                                                                                            cAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAAGAACAAGTTGCAAGCTAATAAACCTTCGCATATGCAAATTATTTg                                                >  2:416835/1‑141 (MQ=255)
                                                                                             aaaCCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAAAGCCCACTTATACGTACATAAAATCACGAATAACGCAATAACAAGTTGCAAAATAATAAACCTTCGCATTTGAAAATTATTTGt                                               >  2:212085/1‑141 (MQ=255)
                                                                                                cccATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGt                                            <  2:331029/141‑1 (MQ=255)
                                                                                                  cATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTa                                          <  1:95536/141‑1 (MQ=255)
                                                                                                  cATATACAAGATTCATGAAGATATGTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAAGCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTa                                          <  1:189074/141‑1 (MQ=255)
                                                                                                      taCAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATc                                      <  2:680049/141‑1 (MQ=255)
                                                                                                             ttGATGATTATATTTGTATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTa                               <  2:548619/141‑1 (MQ=255)
                                                                                                                  gatgatATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAGTTATTTGTCGTTAAATCAATTTTATGCAt                          >  1:354328/1‑141 (MQ=255)
                                                                                                                         ttttGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAAc                   <  2:10266/141‑1 (MQ=255)
                                                                                                                          tttGACCGACATCCGCTGTCACACCTAATGCCCACTTATACGTAAATAAAATCACGAATAGCGCAATAACAAGTTTCAAGATAATAACCTTGCGTATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAAcc                  <  2:677242/141‑1 (MQ=255)
                                                                                                                            tGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAACCCt                <  2:679229/141‑1 (MQ=255)
                                                                                                                              aTCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCACCCCTcc              <  2:337801/141‑1 (MQ=255)
                                                                                                                                cGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAACCCTCCCg            <  1:215960/141‑1 (MQ=255)
                                                                                                                                cGACAACCGCTGTGACACCTAAAGACCACTTATACGTAAATAAACTCACGAATATCGCAAGAACAAGTTGCAAGATAATAATCCTTCGCATTGGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAACCCTCCCg            <  2:112120/141‑1 (MQ=255)
                                                                                                                                    aaCCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTCTGCATTACCAACCCTCCCGATcc        >  2:209028/1‑140 (MQ=255)
                                                                                                                                     aCCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAACCCTCCCGATCAt       <  2:414720/141‑1 (MQ=255)
                                                                                                                                          tgtgACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAACCCTCCCGATCATGACat  <  2:688155/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                          
TATATTAAACATAGGTTTGCTATCTTTTTTAAATAAAAGAAATAATGCTCTATGGATAAGTTCATGTAAAATCAATAAAATAATGAATCCAGCAAACCCATATACAAGATTGATGATGATATTTTGATCGACAACCGCTGTGACACCTAACGCCCACTTATACGTAAATAAAATCACGAATAACGCAATAACAAGTTGCAAGATAATAAACCTTCGCATTTGAAAATTATTTGTCGTTAAATCAATTTTATGCATTACCAACCCTCCCGATCATGACAT  >  USA300TCH1516_ALE/2038104‑2038382

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: ‑