Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,689,552 A→G 13.5% F105S (TTC→TCC)  dnaJ ← Chaperone protein DnaJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,689,5520AG13.5% 117.1 / 7.0 51F105S (TTC→TCC) dnaJChaperone protein DnaJ
Reads supporting (aligned to +/- strand):  ref base A (19/23);  new base G (4/3);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 6.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTTTA  >  USA300TCH1516_ALE/1689418‑1689686
                                                                                                                                      |                                                                                                                                      
cGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGaagaaag                                                                                                                                  <  2:534570/141‑1 (MQ=255)
  cATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGaagaaagat                                                                                                                                >  2:263408/1‑140 (MQ=255)
             tttACCGATTGAAATTTCTTTTGTTTTACCAAATACCGCTTCTTTAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATc                                                                                                                     <  2:130722/141‑1 (MQ=255)
              ttACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCAGCCACCGAAGAAAGAGCTAAAGATATCt                                                                                                                    >  1:482980/1‑141 (MQ=255)
               tACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGGAGAAAGAGCTAAAGGTATCtt                                                                                                                   >  1:668209/1‑141 (MQ=255)
               tACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGGAGAAAGAGCTAAAGATATCtt                                                                                                                   >  1:550659/1‑141 (MQ=255)
               tACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGGAGAAAGAGCTAAAGATATCtt                                                                                                                   >  1:420710/1‑141 (MQ=255)
                 cGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCa                                                                                                                 >  1:118/1‑141 (MQ=255)
                  ggATTGAACTTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGCCTGCCGCCACCGAAGAAAGAGCTAAAGATATCCTCaa                                                                                                                <  1:474418/141‑1 (MQ=255)
                  ggATTGAAATTTCTTTTGTTGTACCAAATACGGCTTCTTCAGATGTTATTGTCCTTTTTTACTGAAGATCATCTCCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCTCCACCGTCGACAGGGCTACAGATCTCTTCaa                                                                                                                >  2:245378/1‑141 (MQ=255)
                           tttCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACcgccgc                                                                                                       <  1:491913/141‑1 (MQ=255)
                              cTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCAc                                                                                                    <  1:259535/141‑1 (MQ=255)
                                   gttgtACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGTTATCTTCAAAACCGCCCCCACCGAAg                                                                                               >  2:572081/1‑141 (MQ=255)
                                       tACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGGGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAACCCAc                                                                                           >  1:621020/1‑141 (MQ=255)
                                          cAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCTCCTaa                                                                                        >  1:156987/1‑141 (MQ=255)
                                            aaTACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACGATTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTaaaa                                                                                      >  2:510162/1‑141 (MQ=255)
                                            aaTACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGAATCTCTTTGTCTTCCGCCACCGAAGAAAGAGCCCAAGATATCTTCATATCCGCCGCCACCGCCGCCACGaaac                                                                                      >  2:122356/1‑140 (MQ=255)
                                                 cGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCCAAACCGCCGCCCCCCAAGCACCTCAAACcccc                                                                                 >  2:611187/1‑141 (MQ=255)
                                                                  aTGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGa                                                                <  1:268067/141‑1 (MQ=255)
                                                                   tGTCATTGTATACTGAAGATCATCACATATTTGCGGAGCATTTGGATCTCATTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCCCCGCCACCGAAGCCACTAAAACCGCCAAAAACAAAGCCATTGaa                                                               >  2:658253/1‑141 (MQ=255)
                                                                     tCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGCTCCCACTCAAACCGCCAAAGTCAGAGCCATTGAATc                                                             <  1:440608/141‑1 (MQ=255)
                                                                      cATTGTTTACTGTAGATCATCTCCTTTTTGAGGTGCATTTGGATCTCTTTGTCCGCCGCCACCGAAGAAAGAGCTAAAGATATCTTTAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATcc                                                            <  2:542224/141‑1 (MQ=255)
                                                                         tGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTg                                                         <  1:284739/141‑1 (MQ=255)
                                                                         tGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTGTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTg                                                         <  2:447778/141‑1 (MQ=255)
                                                                           tataCTGAAGCTCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTc                                                       <  2:481129/141‑1 (MQ=255)
                                                                            ataCTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAACCGGCTAAAGTCAGAGCCAGTGAATCCTTGTcc                                                      <  2:635572/141‑1 (MQ=255)
                                                                            ataCTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTcc                                                      <  1:430311/141‑1 (MQ=255)
                                                                                cgAAGATCATTCCCTGTTGGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATGGAATCCTTGTccacca                                                  <  1:173843/140‑1 (MQ=255)
                                                                                    gATCATCACCTTTTTGCGGTGCATTTGGCTCTCTTTGTCTGCCGCCGCCGAAGCAAGAGCTAAAGATATCTTCAAAACTGGCTCCACCGAAACCACTAAACCCGCCAAAGCCAGATCCATTGAATCCTTGTCAACCACAAc                                              >  1:87849/1‑141 (MQ=255)
                                                                                        atcatcTTTTTGCGGCGCATTTGGATCTCTTTGTCTGCCCACACATATAAAAGACGTAGATAGATCTTCAAAGCCGCCTCCACCGAAACCAGTCAAAAAACCCTGGGCCGAACCATTAAATCCGTTTCAACCAAAAcccta                                          >  2:422948/1‑138 (MQ=255)
                                                                                        atcaCCTTTTTGCGGCGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGACGCCACTAAAACCACCCAAGTCAGAGCTATTCACTCCTTAACACCCAAAAACttt                                          >  2:292577/1‑140 (MQ=255)
                                                                                          caCCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTTTCCACCAACACCTtctg                                        >  2:243016/1‑141 (MQ=255)
                                                                                            ccTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGATTCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGa                                      <  1:95528/141‑1 (MQ=255)
                                                                                             cTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCCCCGGAGGAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGAc                                     >  1:367943/1‑141 (MQ=255)
                                                                                              tttttGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGAcc                                    >  1:401438/1‑141 (MQ=255)
                                                                                              tttttGCGGTGCATTTGGATCTCTTTGCCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGCCCACCAAAACCTCGTGGAcc                                    <  1:436050/141‑1 (MQ=255)
                                                                                              ttttgGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGAcc                                    <  1:244424/141‑1 (MQ=255)
                                                                                                 ttGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACcatc                                 <  2:388004/141‑1 (MQ=255)
                                                                                                     ggTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAATGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCTCCAAAGTCAGAGCCATTGAATCCTTGTCCACCATCACCTTGTGGACCATCATGt                             <  1:451575/141‑1 (MQ=255)
                                                                                                       tGCAATTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAACGATATCTTCCAAACCGCCCCCACCCAAGCCACCAAAACCGCCCAAATCAGACCCAGCGAATCCGTGTCCCACAAAACCTTAAAGACcatcacgctc                           >  2:461684/1‑136 (MQ=255)
                                                                                                         cATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCaa                         >  1:316860/1‑141 (MQ=255)
                                                                                                                   tgttttTCTGCCGCCACCGCAGAAAGAGCTAAAGAAATCTTCAAAACCGCCGCCACCCAAGCCACTAAACCCGCCATAGTCAGAGCCATTGCATCCTTGTCCACCAAAACCTTGCGGACCATCATGTCCAAATTGATCATa               <  2:148430/139‑1 (MQ=255)
                                                                                                                   cctTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATa               <  1:219/140‑1 (MQ=255)
                                                                                                                     tttGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGc             <  2:680806/141‑1 (MQ=255)
                                                                                                                        gTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTg          <  1:565503/141‑1 (MQ=255)
                                                                                                                         tCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTgc         <  2:524386/141‑1 (MQ=255)
                                                                                                                         tCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTgc         <  2:524380/141‑1 (MQ=255)
                                                                                                                          cTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCCCCACCGAAGCCACTAAAACCAACAAAGGCAGACCCATAGAATCCATGTCCTCCAAACACTTGTGGACCATAACATCCAAATAAATCACAGCtccac        >  2:268003/1‑137 (MQ=255)
                                                                                                                              cgccACCGAAGAAAGAGCTAGAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAACCCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGGCCAGCATGTCCGAATTGATAATGGCTTGCGCGtt    >  1:139765/1‑141 (MQ=255)
                                                                                                                              cgccACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAACCCTTGTCCACCAAAACCTCGTGAACCATCATGTCCAAATTGCACATAGCTTACGGGtt    >  2:340906/1‑141 (MQ=255)
                                                                                                                                ccACCGGAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAATCCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTtta  <  2:420710/141‑1 (MQ=255)
                                                                                                                                ccACCGGAGAAAGAGCTAAAGATACCTCCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTtta  <  2:550659/141‑1 (MQ=255)
                                                                                                                                ccACCGGAGAAAGAGCAAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAGACCCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTtta  <  2:668209/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                      
CGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTTTA  >  USA300TCH1516_ALE/1689418‑1689686

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: ‑