Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 427,535 G→A 6.4% Q52* (CAA→TAA)  USA300HOU_0402 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730427,5350GA 6.4% 189.6 / 3.0 62Q52* (CAA→TAA) USA300HOU_0402hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (28/30);  new base A (2/2);  total (30/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.66e-01

GTTTGGAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACATCTCGTTGTATATA  >  CP000730/427398‑427675
                                                                                                                                         |                                                                                                                                            
gTTTGGAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTAc                                                                                                                                           >  1:255972/1‑141 (MQ=255)
 tttGGAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACt                                                                                                                                          >  1:181055/1‑141 (MQ=255)
 tttGGAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACt                                                                                                                                          >  1:180979/1‑141 (MQ=255)
   tGGAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTaa                                                                                                                                        <  1:38004/141‑1 (MQ=255)
    ggAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAAt                                                                                                                                       >  2:410933/1‑141 (MQ=255)
     gAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAAtt                                                                                                                                      <  2:397186/141‑1 (MQ=255)
          tCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGAc                                                                                                                                 >  1:283136/1‑141 (MQ=255)
             cGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTa                                                                                                                              >  2:442318/1‑141 (MQ=255)
              gATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAg                                                                                                                             <  2:217473/141‑1 (MQ=255)
              gATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAg                                                                                                                             >  2:641082/1‑141 (MQ=255)
               aTGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAgg                                                                                                                            >  1:358287/1‑141 (MQ=255)
                   ccTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGCCGTAGGTATc                                                                                                                        >  1:620196/1‑141 (MQ=255)
                   ccTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTATAACAATAATGCATCATCTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATc                                                                                                                        >  1:515793/1‑141 (MQ=255)
                       gCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATcgtcc                                                                                                                    >  2:36019/1‑139 (MQ=255)
                             aCCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTaaaa                                                                                                              >  1:387740/1‑141 (MQ=255)
                               cATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATAATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTCAAAGc                                                                                                            >  1:157393/1‑141 (MQ=255)
                                 tAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCat                                                                                                          <  2:295527/141‑1 (MQ=255)
                                  aGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCata                                                                                                         >  2:668649/1‑141 (MQ=255)
                                        aaaTGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAAtt                                                                                                   <  2:143040/141‑1 (MQ=255)
                                        aaaTGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTATACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAAtt                                                                                                   >  1:324933/1‑141 (MQ=255)
                                        aaaTGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTATACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAAtt                                                                                                   >  1:325128/1‑141 (MQ=255)
                                               tACGTGCATGAGTTGCTTTTTCTATCAATAATTCAGGATAGTGAACGGAGTTAAGAAGAGCGTTATCTAGAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTca                                                                                            <  1:63551/141‑1 (MQ=255)
                                               tACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTca                                                                                            <  1:152295/141‑1 (MQ=255)
                                                 cGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAAtt                                                                                                                                      >  2:618379/1‑97 (MQ=255)
                                                 cGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAAtt                                                                                                                                      <  1:618379/97‑1 (MQ=255)
                                                   tGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATa                                                                                        <  1:380417/141‑1 (MQ=255)
                                                                  ttCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAat                                                                         <  1:2222/141‑1 (MQ=255)
                                                                   tCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAata                                                                        >  1:690458/1‑141 (MQ=255)
                                                                   tCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAata                                                                        <  1:222985/141‑1 (MQ=255)
                                                                    cTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAatat                                                                       >  2:658175/1‑141 (MQ=255)
                                                                        cAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCAtt                                                                   <  2:512193/141‑1 (MQ=255)
                                                                          ataatGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCAtttt                                                                 <  2:669900/141‑1 (MQ=255)
                                                                               gCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCata                                                            <  2:387740/141‑1 (MQ=255)
                                                                                catcatTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCatat                                                           <  1:129290/141‑1 (MQ=255)
                                                                                catcatTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCatat                                                           >  2:482387/1‑141 (MQ=255)
                                                                                     ttttGGACGTTGTTAAGGATAGCTTTATTTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCTACATCCTCTTTCAgattgatt                                                      <  2:122150/141‑1 (MQ=255)
                                                                                       ttGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGAtttg                                                    >  1:411077/1‑141 (MQ=255)
                                                                                       ttGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGAtttg                                                    <  2:318378/141‑1 (MQ=255)
                                                                                             gttgttAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCg                                              <  1:410933/141‑1 (MQ=255)
                                                                                               tgttAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCgtg                                            >  2:582309/1‑139 (MQ=255)
                                                                                               tgttAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTATACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCgag                                            <  2:324933/141‑1 (MQ=255)
                                                                                               tgttAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTATACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCgag                                            <  2:325128/141‑1 (MQ=255)
                                                                                                 ttAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGc                                                                                                            >  2:358774/1‑75 (MQ=255)
                                                                                                 ttAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGc                                                                                                            <  1:358774/75‑1 (MQ=255)
                                                                                                      gATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACa                                     >  1:616429/1‑141 (MQ=255)
                                                                                                          gCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACt                                 >  1:55010/1‑141 (MQ=255)
                                                                                                            tttATCCATAAATAACTGCATAATTGGTTGTACTAATTTACACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTCCGAGCGGTACATACttt                               >  2:240289/1‑141 (MQ=255)
                                                                                                             ttATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTa                              <  1:118425/141‑1 (MQ=255)
                                                                                                             ttATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTa                              <  2:625217/141‑1 (MQ=255)
                                                                                                              gaTCTATAAATATCATCATAATTGAGGGTACGAATATATACGTGGTTATCTGATGTAAAATCAGAAGAGTTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTaa                             <  1:239973/140‑1 (MQ=255)
                                                                                                               aTCTATAAATAACTGCATACTTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCACTATCATTTTTCATATTGCTCGATTTGCGAAAGGTACATACTTTAAg                            >  2:597705/1‑141 (MQ=255)
                                                                                                               aTCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAg                            >  2:238843/1‑141 (MQ=255)
                                                                                                                 cTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCa                          <  1:507691/141‑1 (MQ=255)
                                                                                                                  tataAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCAt                         <  2:283136/141‑1 (MQ=255)
                                                                                                                     aaataaCTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTAt                      <  2:309724/141‑1 (MQ=255)
                                                                                                                        taaCTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGc                   <  1:82008/141‑1 (MQ=255)
                                                                                                                              cATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTATCATATTTATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACAtct             >  1:460410/1‑141 (MQ=255)
                                                                                                                                    tGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACATCTCGTTGt       <  1:60937/141‑1 (MQ=255)
                                                                                                                                    tGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACATCTCGTTGt       <  1:668649/141‑1 (MQ=255)
                                                                                                                                     ggTTGTATAGATGTAGATATAGGTCCCGTACGTAAATGCATAATTGTTGCGTTCTCACAATTTTCATTCTCAAAATCA‑GATTCTTATTGCGTTCTTTGCGATAGGTACATGCTTTAAGCATTATCGCACACCGCGTTGttt     <  2:600823/141‑3 (MQ=255)
                                                                                                                                       ttGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACATCTCGTTGtata    >  2:518850/1‑141 (MQ=255)
                                                                                                                                        tGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACATCTCGTTGtatat   <  1:211451/141‑1 (MQ=255)
                                                                                                                                         gTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACATCTCGTTGtatata  <  1:577975/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                            
GTTTGGAATGTCACGATGACCTTGCAATGACCATAGACGTAAATGATTACGTGCATGAGTTGCTTTTTCTATCAATAATGCATCATTTTGGACGTTGTTAAGGATAGCTTTATCTATAAATAACTGCATAATTGGTTGTACTAATTTAGACGTAGGTATCGTACGTAAAAGCATAATAATTTCGTTCACATACTTTTCTTTCTCAATATCATTTTTCATATTGATTTGTTTGCGAGAGGTACATACTTTAAGCATTATCGCACATCTCGTTGTATATA  >  CP000730/427398‑427675

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑