Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,470,111 G→A 54.9% S575L (TCA→TTA)  USA300HOU_2333 ← MFS family major facilitator transporter, multidrug:cation symporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,470,1110GA54.9% 3.4 / 64.1 49S575L (TCA→TTA) USA300HOU_2333MFS family major facilitator transporter, multidrug:cation symporter
Reads supporting (aligned to +/- strand):  ref base G (13/9);  new base A (9/18);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 8.95e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.90e-01

AATAAACATAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAATTG  >  CP000730/2469976‑2470247
                                                                                                                                       |                                                                                                                                        
aaTAAACATAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACCCTTTCATTTCGCCTTCTTGTCCGCCATATTGTAATGCt                                                                                                                                     >  2:272344/1‑141 (MQ=255)
       agaagaTTAAGGCGATGATGCTAAATAGCGTTGCAACTATAAGTGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCAt                                                                                                                              <  2:339771/136‑1 (MQ=255)
        tAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATg                                                                                                                             <  1:551591/141‑1 (MQ=255)
         aaaaTTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGc                                                                                                                            <  2:513859/141‑1 (MQ=255)
              tAAGTCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATg                                                                                                                       <  1:29723/141‑1 (MQ=255)
               aaGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCGTTGCGCCGTCTTGTCCGACATCTTGTGCTGCTCATTCACGCATCTgc                                                                                                                      >  2:195574/1‑140 (MQ=255)
                 ggCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATc                                                                                                                    >  1:66759/1‑141 (MQ=255)
                       gatgCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGtca                                                                                                              >  2:198864/1‑139 (MQ=255)
                       gatgCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAAACGTTGCCCGTATATTTCCAAATTGTAGTCATACTTTCCTGGCGCCTTCTTGTCCGCCGGATAGTAATGCTAAGTCATTCATATGATCTTGtcc                                                                                                              >  2:331575/1‑139 (MQ=255)
                            tAAATATCGTTGTAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAATTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATAGTGATGCTAATTCATGCATATGATCTTGTACAACAg                                                                                                         <  1:394979/141‑1 (MQ=255)
                             aaaTATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAgg                                                                                                        <  1:237198/141‑1 (MQ=255)
                                   cGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGt                                                                                                  <  2:382399/141‑1 (MQ=255)
                                        cAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTAt                                                                                             <  2:387198/141‑1 (MQ=255)
                                              taAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAAct                                                                                       >  2:358967/1‑141 (MQ=255)
                                                   tcatcatTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTcc                                                                                  <  1:516105/140‑1 (MQ=255)
                                                   gCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGACTTCTTGTCCGCCATATTGTAATGCTAATTCATGTATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTcc                                                                                  <  1:384675/141‑1 (MQ=255)
                                                          tAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAg                                                                           >  1:480306/1‑141 (MQ=255)
                                                            aTACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCt                                                                         >  2:368036/1‑141 (MQ=255)
                                                            aTACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCt                                                                         <  1:506429/141‑1 (MQ=255)
                                                             tACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAATACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTg                                                                        <  1:26866/141‑1 (MQ=255)
                                                                         ttGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTtgtg                                                            >  1:207828/1‑141 (MQ=255)
                                                                             tAGTTTATTTACAAATTGTATTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGt                                                        <  2:142676/141‑1 (MQ=255)
                                                                                tttatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAATAGCTGATAAGTGTTGTGTTGTTtg                                                     >  1:353249/1‑141 (MQ=255)
                                                                                tttatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTtg                                                     >  2:356245/1‑141 (MQ=255)
                                                                                  tatttaCAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTtgtg                                                   <  1:53272/141‑1 (MQ=255)
                                                                                         aaaTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCAt                                            >  1:496209/1‑141 (MQ=255)
                                                                                         aaaTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCAt                                            >  2:181670/1‑141 (MQ=255)
                                                                                           aTTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTa                                          <  2:325252/141‑1 (MQ=255)
                                                                                                  taACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTTTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTTTCTAGTTTGTGTTGTCATTTCAATAAc                                   >  2:112295/1‑141 (MQ=255)
                                                                                                  taACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCCTTACAGTagc                                   >  1:220603/1‑139 (MQ=255)
                                                                                                   aaCACTTTCATTGGCCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACt                                  <  2:217970/141‑1 (MQ=255)
                                                                                                      ccTTTCATTGCGCCTTCTTGTCCGCCATATTTTAATGCTTATTTATGCATAAGTACTTGTACAACAGGATTCGTATTATTTAACTCTTCCTCAAAAGCTGATTAGTGTTTTTTAGTTTGTGTTGTCATTACAGTATCTAAg                               <  2:253118/140‑1 (MQ=255)
                                                                                                       cTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                              <  1:160335/141‑1 (MQ=255)
                                                                                                       cTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                              >  1:175593/1‑141 (MQ=255)
                                                                                                       cTTTCATTGCGCCTTCTTGGCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGa                              <  1:192173/141‑1 (MQ=255)
                                                                                                        tttCATTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAACGCGGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGAt                             <  1:323265/141‑1 (MQ=255)
                                                                                                            aTTGCGCCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGGTAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCt                         >  1:482136/1‑141 (MQ=255)
                                                                                                              tGCCCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTGCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGt                       <  1:426764/141‑1 (MQ=255)
                                                                                                               gcgcCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTa                      >  1:567504/1‑141 (MQ=255)
                                                                                                                 gcCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTAcc                    >  2:523831/1‑141 (MQ=255)
                                                                                                                 gcCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGATTTATCTAACTCTTCCCCAAAAGCAGATCAGTGTTGTGTGGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTAcc                    >  2:197433/1‑141 (MQ=255)
                                                                                                                 gcCTTCTTGTCCGCCATATTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTAcc                    <  1:368036/141‑1 (MQ=255)
                                                                                                                    ttcttGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCtat                 <  1:67343/141‑1 (MQ=255)
                                                                                                                        tGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTGGTAAAACAGGATTCGTTTTATCTAACTCTTACCCAAAAGCTGATAAGTGTTCTGTAGTTTGTGTTGTCATTACAGTAACTAAGAGTGCTGTAACTATagag             >  2:243833/1‑141 (MQ=255)
                                                                                                                           ccGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCt          <  2:362767/141‑1 (MQ=255)
                                                                                                                                atatTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTaa     <  2:4604/141‑1 (MQ=255)
                                                                                                                                 tatTGTAATGCTAATTGCTGCATTTGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAt    <  1:413669/141‑1 (MQ=255)
                                                                                                                                 tatTGTAATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTTTTCTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAAt    <  1:413827/141‑1 (MQ=255)
                                                                                                                                   ttGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTACTGTACCTATAGAGCCTACTGATTg  >  2:117580/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                        
AATAAACATAAAATTAAGGCGATGATGCTAAATATCGTTGCAACTATAAATGCATCATTAATACCTTCAACCGTTGCTAGTTTATTTACAAATTGTAGTAACACTTTCATTGCGCCTTCTTGTCCGCCATATTGTGATGCTAATTCATGCATATGATCTTGTACAACAGGATTCGTTTTATCTAACTCTTCCCCAAAAGCTGATAAGTGTTGTGTAGTTTGTGTTGTCATTACAGTAACTAAGATTGCTGTACCTATAGAGCCTGCTAATTG  >  CP000730/2469976‑2470247

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: ‑