Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,513,930 A→T 100% L413F (TTA→TTT USA300HOU_1379 → hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,513,9300AT100.0% 184.1 / ‑6.5 63L413F (TTA→TTTUSA300HOU_1379hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  major base T (30/31);  minor base G (1/0);  total (31/32)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  CP000730/1513792‑1514066
                                                                                                                                          |                                                                                                                                        
tAATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTAAATCACTAATAATATGATTTAt                                                                                                                                        >  2:73848/1‑141 (MQ=255)
    ttatttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTa                                                                                                                                    >  2:1036382/1‑141 (MQ=255)
            atgtagTGCTTTATTAGGAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACTATCATCTATATCACTCATAATATGTTTTTTTGTATTAGGatt                                                                                                                            <  2:254861/141‑1 (MQ=255)
            atgaaccGCTTTATGAGTAGCTAGTGGCATGGGGTTTGTCTCTTGGATAAAGCGAACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAGACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGatt                                                                                                                            <  2:199863/135‑1 (MQ=255)
              gtagCGCTTTATTAGGAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCACTAAAAGTACCACATCGCGTAAAAAAACCCGCATCCATATCCCTCATAATATGTTTTATTGTATTAGGattat                                                                                                                          <  2:887749/141‑1 (MQ=255)
                   gttttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTAAAAAAAATACTTCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                     <  2:793872/139‑1 (MQ=255)
                   gCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                     >  2:338765/1‑141 (MQ=255)
                    cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAACAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGc                                                                                                                    >  1:411387/1‑141 (MQ=255)
                        attaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatt                                                                                                                <  1:697353/141‑1 (MQ=255)
                         ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTGAAAAAAATACTGCAATAAAAGTACCACCTAGCGTACAATAACAAGCAACCAAACTACTCTTTATAGGTTTGATGATTTTTGGATTTTTAATGCCattt                                                                                                               >  2:615794/1‑140 (MQ=255)
                          tagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattat                                                                                                              >  1:320038/1‑141 (MQ=255)
                           agtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCattatt                                                                                                             <  1:867166/141‑1 (MQ=255)
                             tagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                           <  1:697114/141‑1 (MQ=255)
                              acccATTGGCATGGGGTTTGTCTCCTGGATAAAGCGTACAAAAAATACTGCAATAAAACTACCACATCCCGTAACAACACCAACACCGATACCACCCTTAATATGTCTAATTTTATTACGATTATTACCGCCCTTCtttcg                                                                                                          <  2:312844/139‑3 (MQ=255)
                                ccATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACACAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGAt                                                                                                        <  1:306200/141‑1 (MQ=255)
                                  aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                                      >  1:88192/1‑141 (MQ=255)
                                   ttGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                     <  1:428349/141‑1 (MQ=255)
                                    tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGAGTTATTAATGCCATTATTTGGATTATc                                                                                                    >  1:651493/1‑141 (MQ=255)
                                     ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTCTTAATGCCATTATTTGGATTATCa                                                                                                   <  1:675064/141‑1 (MQ=255)
                                      gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                                  <  1:162397/141‑1 (MQ=255)
                                      gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                                  >  1:309481/1‑141 (MQ=255)
                                          ggggTTTTTCTCTCGGATAAAGCGTACAAAAAATACTTCAATAAAAGTACCTCATCGCGTAAGAATACCAGCATCTATATGTCTCATAATATGCTTTATGGTATTAGGATTATTAATGCCATTCTTTGGTTTTTCACTTAt                                                                                              <  2:46070/141‑1 (MQ=255)
                                           gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                                                             >  1:25564/1‑141 (MQ=255)
                                           gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAAGAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGAATTATCACTTATc                                                                                             >  2:957390/1‑141 (MQ=255)
                                             gTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCATAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCt                                                                                           <  1:940820/141‑1 (MQ=255)
                                                 tgctctgtatcaaaGCGGAAAAAAAATACTGTAATAAAAATACCACATCGCATAAAAAAACCAGCATTTATATCACTCATAATATTTTTTTGTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                       <  2:166042/130‑1 (MQ=255)
                                                  tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                      <  1:805428/141‑1 (MQ=255)
                                                            aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                            <  1:700362/141‑1 (MQ=255)
                                                             aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTAGAATAACACTTATCCTTGTATTTATAATTaaa                                                                           >  2:398932/1‑141 (MQ=255)
                                                              aGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                          <  2:583041/141‑1 (MQ=255)
                                                               gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                         <  1:851665/141‑1 (MQ=255)
                                                               gCGTACAAAAAATACTGCAATAAAAGTACCACATCACGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATTACTTATCCTTGTATTTAAAGTTGAAtt                                                                         >  1:867680/1‑141 (MQ=255)
                                                               acatACAAAAAATACTTCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                         <  2:191444/138‑1 (MQ=255)
                                                                 gTACAAAAAATACTGCAATAAAAGTAACACATCGCGTAAAAAAAACAGCATCTATATCCCTCATAATATGTTATATTGTATTAGGATTATTAATTCCAATATTTGGATTATCAGTTATCCTTGTATTTACAATTGAAttta                                                                       >  2:104089/1‑139 (MQ=255)
                                                                       aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATtattattat                                                                 >  2:607987/1‑141 (MQ=255)
                                                                       aaaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCACATATATCACACATAATATGTAGTATTGTATTAGGAATATTAAGGCCAGTAGTTGGATTATCACTTATCCTTGTATTTATAATGGAATTAAtattat                                                                 >  2:522618/1‑141 (MQ=255)
                                                                           tACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTatatat                                                             >  2:137799/1‑141 (MQ=255)
                                                                             atGCAATAAAAGTACCACACCGCGTAAAAAAGCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTa                                                           <  2:654376/140‑1 (MQ=255)
                                                                              tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                          <  2:320038/141‑1 (MQ=255)
                                                                              tGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaa                                                          >  1:27782/1‑141 (MQ=255)
                                                                               gCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTCATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaca                                                         >  1:212575/1‑139 (MQ=255)
                                                                               gCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATCAAAAATATTaaa                                                         >  2:216654/1‑141 (MQ=255)
                                                                               gCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATTTTaaa                                                         >  2:89223/1‑141 (MQ=255)
                                                                                     aaaGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTagaagtcgt                                                   >  2:839325/1‑133 (MQ=255)
                                                                                     aaaGTACCACATCGCATAAAAAAACCAGCATCCATAGCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                                   <  2:9144/141‑1 (MQ=255)
                                                                                        gTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATcgtcgt                                                >  1:577334/1‑141 (MQ=255)
                                                                                          aCCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGc                                              >  1:851643/1‑141 (MQ=255)
                                                                                               aTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                                         >  1:170018/1‑141 (MQ=255)
                                                                                               aTCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                                         <  2:826142/141‑1 (MQ=255)
                                                                                                tCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAAATCGTCGTGCTAACCa                                        >  2:57752/1‑141 (MQ=255)
                                                                                                gcgcgTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACa                                        <  1:350873/140‑1 (MQ=255)
                                                                                                     tAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataat                                   >  2:385115/1‑141 (MQ=255)
                                                                                                        aaaaaCCAGCATCTATATCACTCATAATCTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                                >  2:180342/1‑141 (MQ=255)
                                                                                                        aaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                                >  2:497176/1‑141 (MQ=255)
                                                                                                         aaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCAc                               <  2:25564/141‑1 (MQ=255)
                                                                                                          aagccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACt                              <  2:188702/138‑1 (MQ=255)
                                                                                                                gCATCTATATCACTCATAATATGTTTTATTGTATTAGGAATATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGGGCTAAACAATAATGCACTTAAAGt                        >  2:664099/1‑141 (MQ=255)
                                                                                                                 cATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                       <  1:855791/141‑1 (MQ=255)
                                                                                                                               ataataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGaaa         <  1:229918/141‑1 (MQ=255)
                                                                                                                                taatgTGTTATAATGTATTAGGATTATTAATTCCATTATTTGGATTATCACTTATCCTTGTATTTATACTTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt        <  2:867680/141‑1 (MQ=255)
                                                                                                                                    ttGTTTTATTGTATTATGATTATTAATGCCATTATTTGGATTATGACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc    <  2:708314/140‑1 (MQ=255)
                                                                                                                                    atGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc    <  2:955291/141‑1 (MQ=255)
                                                                                                                                      gTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTAAACTGACGAAATTTaaaa  >  1:155952/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                        
TAATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTACAA  >  CP000730/1513792‑1514066

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: