Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 396,540 G→A 100% A208T (GCA→ACA)  USA300HOU_0364 → possible lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730396,5400GA100.0% 153.4 / ‑6.5 51A208T (GCA→ACA) USA300HOU_0364possible lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (25/25);  total (26/25)
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.

GATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGT  >  CP000730/396408‑396675
                                                                                                                                    |                                                                                                                                       
gagatgaTACCAAAAATAATGCTACAAGTTTCTGTTGACCTATTAAATGAAGCTCTAACTACTAAAAACACAGGTGAAGAAGCAATATATTCACATACCGATTTGTAAGATTTTAAACCGAGCGTTGAAGCcacacacag                                                                                                                                  <  2:257009/134‑4 (MQ=255)
     cATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAttt                                                                                                                             >  2:135738/1‑140 (MQ=255)
     cATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAttt                                                                                                                             >  1:165797/1‑140 (MQ=255)
     cATACCAAAATTAATGTTACAAGGTTCTGTTGAACTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAGAAAAttt                                                                                                                             <  2:64681/140‑1 (MQ=255)
      aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTa                                                                                                                            <  2:452171/140‑1 (MQ=255)
      aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTa                                                                                                                            <  2:217977/140‑1 (MQ=255)
        aCCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAGTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATg                                                                                                                          >  1:332221/1‑140 (MQ=255)
         ccAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAAGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGa                                                                                                                         >  2:153234/1‑140 (MQ=255)
          cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                        <  1:217661/140‑1 (MQ=255)
             aaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACttc                                                                                                                     >  2:518965/1‑139 (MQ=255)
             aaTTAATGTTACAAGGTACTGTTGACCTATTAAATAAAGTGGCAACTTCTAAAAACACAGGTCAAGAAGAAATTTATTCACAAACAGATTTATATGATTTTAAAGGGAACGTTAAAGGCACACAAAAAATTTATGACTTa                                                                                                                     >  2:174816/1‑140 (MQ=255)
                   tGTTTCAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaaa                                                                                                               <  2:441699/140‑1 (MQ=255)
                      tACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCt                                                                                                            <  2:386800/140‑1 (MQ=255)
                            gTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTa                                                                                                      <  1:80789/140‑1 (MQ=255)
                             ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                     >  1:393124/1‑140 (MQ=255)
                             ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                     <  2:80198/140‑1 (MQ=255)
                             ttCTGTTGACCTATTAAATGAAGTTGCAACTTATAATATCACAGGTGAAGAAGAAATTTATTCAAATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAATCAGGTAAGACGTATTTAAACCTATTTTag                                                                                                     <  1:131566/140‑1 (MQ=255)
                                 gTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGCAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAACTATTTTATAGaa                                                                                                 >  2:164059/1‑140 (MQ=255)
                                 gTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaa                                                                                                 >  1:436878/1‑140 (MQ=255)
                                  ataaCCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGGGAAGAAGAAATTTATTCACATACAGCTTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATATATGACTTAGTTAAACCTATTTAAGGGaaa                                                                                                >  2:452696/4‑140 (MQ=255)
                                       cTATTAAATGAAGTTGCAACTTCTAACATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                           <  2:193916/140‑1 (MQ=255)
                                       atATTAAATGAAGTTGCAACTTATAAAATAACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                           <  1:250056/139‑1 (MQ=255)
                                          ttAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaa                                                                                        >  1:515158/1‑140 (MQ=255)
                                              aTGAAGTTGCAACTTCTAAAATCACAGGTGAATAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                    <  1:314010/140‑1 (MQ=255)
                                              aTGAAGGTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                    <  2:466026/140‑1 (MQ=255)
                                                gAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAAAGAAAAAAGATAAAAAAtt                                                                                  >  1:364203/1‑140 (MQ=255)
                                                  aGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAGTTaa                                                                                >  2:399953/1‑140 (MQ=255)
                                                      gCAACTTCTAAAATCCCGAGAAAATGAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATAACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtga                                                                            >  2:530184/1‑140 (MQ=255)
                                                       cAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                           <  2:500190/140‑1 (MQ=255)
                                                         aCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatga                                                                         >  2:394255/1‑140 (MQ=255)
                                                               aaaaTCACAGGTGAAGAAGAAATTTAATCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCa                                                                   >  2:330563/1‑140 (MQ=255)
                                                                aaaTCAGAGGGGAATAAGAAATTTATTCACATATAGAGTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAATATTAAGTGATGATATCCaa                                                                  <  2:446881/140‑1 (MQ=255)
                                                                 aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAATCAAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAATTGATGATATCCaaa                                                                 <  1:288022/140‑1 (MQ=255)
                                                                 aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaa                                                                 <  2:52300/140‑1 (MQ=255)
                                                                             agaagaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTTAAGGCACACAAAACATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATa                                                     >  1:121949/1‑140 (MQ=255)
                                                                                    aTTTATTCACATACAGATTTATATGATTTTAAAACGAACGGTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGaa                                              <  1:511352/140‑1 (MQ=255)
                                                                                        aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCaa                                          <  2:165103/140‑1 (MQ=255)
                                                                                          tCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGTGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAatt                                        <  2:108996/140‑1 (MQ=255)
                                                                                            acaTACAGATTTATATTATTTTAAAGCGAAAGATGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTaaaaaaaaaat                                      <  2:165797/140‑9 (MQ=255)
                                                                                             caTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGATAAAAAAGATAAAAAATTAAGTGATGCTATCCAAATGAACTTCGATAAAGTGAATCAattatt                                     <  1:289341/140‑1 (MQ=255)
                                                                                                 cAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGAt                                 <  1:219858/140‑1 (MQ=255)
                                                                                                   gATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAACATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGAAAAAAAATAAAGTGATGATATCCAAATAAACTTCGATAAAGTGAATCACTTATGGGATaa                               >  1:36835/1‑140 (MQ=255)
                                                                                                             aTTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATGATTGGAAAAATATAAAGAt                     >  2:51697/1‑140 (MQ=255)
                                                                                                             aTTTTAAAGCGAACGTTGAAGGCACACAAAAAATGTATGACTTATTTAAACCTATTTGAGATAAACAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATCATTGGATAAACATAAAGAt                     >  2:407241/1‑140 (MQ=255)
                                                                                                                 tAAAGCGAACGTTGAAGGCACACAAAAAATGTATGACTTAGTGAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTTATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaaca                 <  1:12981/140‑1 (MQ=255)
                                                                                                                  aaaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaa                >  1:222075/1‑140 (MQ=255)
                                                                                                                   aaGCGAACGTTGAAGGCACACAAAAAATTTATGCCTTATTTGAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaaaaac               >  2:90547/1‑140 (MQ=255)
                                                                                                                   aaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaac               <  1:135738/140‑1 (MQ=255)
                                                                                                                     gCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAACGATAACAAcgg             >  2:202949/1‑140 (MQ=255)
                                                                                                                            ttGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTAt      >  1:530499/1‑140 (MQ=255)
                                                                                                                            ttGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGACGGTGAt      >  2:487212/1‑140 (MQ=255)
                                                                                                                                aGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATCAAGTGAATCAATTATTTGATAAATATAAAGATAACAACGACGGTTATGAGt  >  1:512684/1‑140 (MQ=255)
                                                                                                                                    |                                                                                                                                       
GATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGT  >  CP000730/396408‑396675

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: ‑