Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,301,747 T→C 9.5% S442S (TCA→TCG)  USA300HOU_2160 ← MFS family major facilitator transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,301,7470TC 9.5% 128.3 / 3.8 51S442S (TCA→TCG) USA300HOU_2160MFS family major facilitator transporter
Reads supporting (aligned to +/- strand):  ref base T (20/26);  new base C (2/3);  total (22/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTTTAAGATAATTCACAATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTATCGCATAAAGATATCCCATTATTGTTGAACCT  >  CP000730/2301608‑2301885
                                                                                                                                           |                                                                                                                                          
tGTTGAAGATAATTCACAATCATTGGCCTCCTTATGAATAAAATATTGAACGATTTATCTAGTATCTAGGAATTTTATTATTTCTTACTTTAATGACATTACATCAATTTTAATCATAATTCTATTCTTTTGCGTGAGATg                                                                                                                                           >  2:136456/1‑141 (MQ=255)
       gATAATTCACAATCATTGTCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTAGTTCTTACTTTAATTACGCGACATCAATTTGAAGCATAATTCTATTCTTTTGATTGAGATGACTGTTc                                                                                                                                    <  2:153299/141‑1 (MQ=255)
          aaTTCAAAATAATTGGCCTACTTATTAATAAAATAATGAAAAATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCttt                                                                                                                                 <  1:199113/141‑1 (MQ=255)
           aTTCACAATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTa                                                                                                                                >  1:91650/1‑141 (MQ=255)
            ttCACAATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTaa                                                                                                                               <  1:91540/141‑1 (MQ=255)
             tCACAATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGACGACTGTTCTTTaaa                                                                                                                              >  2:170496/1‑141 (MQ=255)
             tCACAATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGACGACTGTTCTTTaaa                                                                                                                              >  2:170495/1‑141 (MQ=255)
               acaATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTaaaaa                                                                                                                            <  1:235551/141‑1 (MQ=255)
                caATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTaaaaaa                                                                                                                           >  2:457524/1‑141 (MQ=255)
                caATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTaaaaaa                                                                                                                           >  2:216044/1‑141 (MQ=255)
                     aTTGGCCTCCTTATTAATACTATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGa                                                                                                                      <  1:229794/141‑1 (MQ=255)
                     aTTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACgc                                                                                                                      >  2:285559/1‑140 (MQ=255)
                     aTTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGa                                                                                                                      >  2:285548/1‑141 (MQ=255)
                      ttGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGAc                                                                                                                     >  2:209730/1‑141 (MQ=255)
                        ggCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTT‑AAAAATACGACCCa                                                                                                                  >  1:313026/1‑141 (MQ=255)
                             cctTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATaaa                                                                                                              <  1:45676/141‑1 (MQ=255)
                             cctTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATaaa                                                                                                              <  2:32338/141‑1 (MQ=255)
                              ctTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGATCATAAAAAAATACGACCCATaaaa                                                                                                             <  2:320402/141‑1 (MQ=255)
                                  ttaATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAAt                                                                                                         <  1:14584/141‑1 (MQ=255)
                                  ataataaCAGATTGAACGATTTATCTAGTATCTATGAAATTTATTATTTCTTACTTTAATTACACAACTTCAGTCTTAAACATAAGTCTATTCTTTTGCATGAAACAACGCTTCTGTAAGCAATATGACCCAttcgccaat                                                                                                         <  2:208500/140‑9 (MQ=255)
                                     ataaAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAg                                                                                                      >  1:361732/1‑141 (MQ=255)
                                       aaaaTATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGcc                                                                                                    <  2:413986/141‑1 (MQ=255)
                                        aaaTTTTGAACTATTTATTCAGCATCTAGGCAATTTATTATTTCTTACTTTAATTACAGTACATCAATTTTAATTTTAATTCTATGCTTTTGACTGAGATGACTGTTCTTTAAAAAAGATGACCCATAAAACAATAAAccc                                                                                                   >  2:32326/1‑141 (MQ=255)
                                           tatTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAAt                                                                                                <  2:356888/141‑1 (MQ=255)
                                                          ctagtatctagGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTacagcaac                                                                                 <  2:116138/141‑1 (MQ=255)
                                                          ctagtatctagGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTacagcaac                                                                                 <  2:116058/141‑1 (MQ=255)
                                                          ctagtatctagGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTacagcaac                                                                                 >  2:346804/1‑141 (MQ=255)
                                                                  tagGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTa                                                                         >  1:142772/1‑141 (MQ=255)
                                                                  tagGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTa                                                                         >  1:150040/1‑141 (MQ=255)
                                                                    ggAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAac                                                                       >  2:292912/1‑141 (MQ=255)
                                                                             ttattTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCAT‑AAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTa                                                             >  2:121754/1‑141 (MQ=255)
                                                                              tattTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTa                                                             >  1:93593/1‑141 (MQ=255)
                                                                                tttCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAg                                                           <  2:86708/141‑1 (MQ=255)
                                                                                  tCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGtt                                                         <  2:124785/141‑1 (MQ=255)
                                                                                  tCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGtt                                                         >  2:433013/1‑141 (MQ=255)
                                                                                      aCTTTAATTACACTACACCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGa                                                     >  1:134716/1‑141 (MQ=255)
                                                                                         ttAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCa                                                  >  2:381828/1‑141 (MQ=255)
                                                                                             ttACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGa                                              <  2:35148/141‑1 (MQ=255)
                                                                                             ttACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGa                                              <  1:153787/141‑1 (MQ=255)
                                                                                                   tACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTg                                        <  1:457524/141‑1 (MQ=255)
                                                                                                     cATCAATTTTAATCATAATTCTATTCTTTTGATTGAGACGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGAt                                      <  1:170496/141‑1 (MQ=255)
                                                                                                     cATCAATTTTAATCATAATTCTATTCTTTTGATTGAGACGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGAt                                      <  1:170495/141‑1 (MQ=255)
                                                                                                      aTCAATTTTAATCATAATTCTATTCTCTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGAtt                                     <  2:87826/141‑1 (MQ=255)
                                                                                                         aaTTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTa                                  <  1:112181/141‑1 (MQ=255)
                                                                                                          aTTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTAt                                 <  1:365665/141‑1 (MQ=255)
                                                                                                                       ttctattctTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGTTTGTATCGCATAAAGatat                    <  1:237904/141‑1 (MQ=255)
                                                                                                                        tctattctTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTATCGCATAAAGATATc                   <  2:220907/141‑1 (MQ=255)
                                                                                                                          tattctTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTATCGCATAAAGATATccc                 <  1:129513/141‑1 (MQ=255)
                                                                                                                            ttctTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTATCGCATAAAGATATCCCat               >  1:248665/1‑141 (MQ=255)
                                                                                                                                         gaTGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTATCGCATAAAGATATCCCATTATTGTTGAACCt  <  1:430802/141‑1 (MQ=255)
                                                                                                                                         gaTGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTATCGCATAAAGATATCCCATTATTGTTGAACCt  <  2:77860/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                          
TGTTTAAGATAATTCACAATCATTGGCCTCCTTATTAATAAAATATTGAACGATTTATCTAGTATCTAGGAAATTTATTATTTCTTACTTTAATTACACTACATCAATTTTAATCATAATTCTATTCTTTTGATTGAGATGACTGTTCTTTAAAAAATACGACCCATAAAACAATAAGCCCAATGCTAATTACAGCAACAGCACTTAACACATTGTGTAAGTTTGGACCAAAGATTCCTGATTGTATCGCATAAAGATATCCCATTATTGTTGAACCT  >  CP000730/2301608‑2301885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑