Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 39,378 C→A 43.3% D586Y (GAT→TAT)  mecA ← penicillin binding protein 2 prime

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073039,3780CA43.3% 24.5 / 26.3 36D586Y (GAT→TAT) mecApenicillin binding protein 2 prime
Reads supporting (aligned to +/- strand):  ref base C (10/10);  new base A (10/6);  total (20/16)
Fisher's exact test for biased strand distribution p-value = 5.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCAT  >  CP000730/39241‑39512
                                                                                                                                         |                                                                                                                                      
aaTAGTCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATAtcttc                                                                                                                                     >  2:283892/1‑141 (MQ=255)
 aTAGCGATCATCATGTTTGGATTATCCTTATCATATGATATAAACCTCCCCATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCACTAACGGATTTTCCAATTAAGTTTGCATAAGATCTATAAATAtattct                                                                                                                                    <  2:226490/141‑1 (MQ=255)
   agtcatcatcatGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCttt                                                                                                                                  <  2:208506/138‑1 (MQ=255)
    gCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTa                                                                                                                                 >  1:104871/1‑141 (MQ=255)
      caatatcatTTTTTGATTATCTTTATCATAAGATATATAAAACCAGATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTAtg                                                                                                                               <  1:94102/137‑1 (MQ=255)
            catGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTAGAGTTCTGTAGAACAGGAGAGGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGtttt                                                                                                                         >  1:149060/1‑141 (MQ=255)
              tGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTtttat                                                                                                                       >  1:345097/1‑141 (MQ=255)
               gTTTGGATTATCTTCATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTtttatt                                                                                                                      >  2:234180/1‑141 (MQ=255)
                       tATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACtt                                                                                                              >  1:336466/1‑141 (MQ=255)
                              aTCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCAt                                                                                                       <  2:32234/141‑1 (MQ=255)
                              aTCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCAt                                                                                                       <  2:106087/141‑1 (MQ=255)
                                   atGATAGAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCAt                                                                                                  <  2:221019/141‑1 (MQ=255)
                                          aaaCCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTaa                                                                                           >  2:297040/1‑141 (MQ=255)
                                                    aTTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGata                                                                                 >  1:300294/1‑141 (MQ=255)
                                                    aTTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGata                                                                                 >  2:45776/1‑141 (MQ=255)
                                                    aTTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGata                                                                                 >  2:148594/1‑141 (MQ=255)
                                                                     tcCTTGTTTCCTTTTGATTTCTGCCGTACCGGATTTGCTAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTTTGTTTTTTATTTACGATTTGTTGCATACCATCATTTAATAGATTGATATTTTCTTTGGAaataat                                                                <  2:8081/141‑1 (MQ=255)
                                                                     tcCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAaataat                                                                >  1:174099/1‑141 (MQ=255)
                                                                      ccTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTGATAGATTGATATTTTCTTTGGAAataata                                                               >  2:20017/1‑141 (MQ=255)
                                                                      ccTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGGTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAataata                                                               <  1:335731/141‑1 (MQ=255)
                                                                             tCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATGTTATTTttct                                                        >  2:161585/1‑141 (MQ=255)
                                                                                ttttGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAACTAATATTttccttcc                                                     <  2:45655/141‑1 (MQ=255)
                                                                                     aGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACt                                                <  1:148594/141‑1 (MQ=255)
                                                                                      gTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACtt                                               >  1:100583/1‑141 (MQ=255)
                                                                                       ttCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACttt                                              >  1:261338/1‑141 (MQ=255)
                                                                                         cTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGt                                            <  1:293478/141‑1 (MQ=255)
                                                                                                aCCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTGGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgt                                     <  2:56600/141‑1 (MQ=255)
                                                                                                 ccGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCgtt                                    >  2:48292/1‑140 (MQ=255)
                                                                                                    gATTTGCCAATTAAGTTTGCATAACATCTATAAATATCTTCTTTATGTGTTTCATTTACGACTTCTTGCATACCCTCACTTAATAGATTGCTATTTTCTTTGGACATAATATTTTTCTTCCACACCTTGCTCTTCGTGTCt                                 >  2:115727/1‑141 (MQ=255)
                                                                                                     aTTTGCCAATTAAGTTTGCGTAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCtt                                >  1:188804/1‑141 (MQ=255)
                                                                                                     aTTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCtt                                >  1:271899/1‑141 (MQ=255)
                                                                                                          ccAATTAAGTTTGCATAAGATCTATAAATATATTCTTTATGTGTTTTATTTACGCCTTGTTGCATACCATCACTTAAAAGATTGGTATTTTCTTTGGTAATAATATTTTTATTGACAACATTGTTTTTCgtatttatttaa                           >  2:267644/1‑131 (MQ=255)
                                                                                                           cAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTtaata                          <  1:236429/141‑1 (MQ=255)
                                                                                                                       cATAATATCTATAAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCCTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGt              <  1:217380/141‑1 (MQ=255)
                                                                                                                                tataAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGc     <  2:336466/141‑1 (MQ=255)
                                                                                                                                 ataAATATATTCTTTATGTGTTTTATTTACGACTTGTTGCTTACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGcc    <  2:104871/141‑1 (MQ=255)
                                                                                                                                   aaaTATCTTCTTTATGTGTTTTATTTAACACTAGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAACCTTTGTTTTTCGTGTCTTTTAATCGGTGAGGTGGGTTAATATTTCCat  >  1:82025/1‑141 (MQ=255)
                                                                                                                                   aaaTATATTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCat  <  1:20017/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                      
AATAGCCATCATCATGTTTGGATTATCTTTATCATATGATATAAACCACCCAATTTGTCTGCCAGTTTCTCCTTGTTTCATTTTGAGTTCTGCAGTACCGGATTTGCCAATTAAGTTTGCATAAGATCTATAAATATCTTCTTTATGTGTTTTATTTACGACTTGTTGCATACCATCAGTTAATAGATTGATATTTTCTTTGGAAATAATATTTTTCTTCCAAACTTTGTTTTTCGTGTCTTTTAATAAGTGAGGTGCGTTAATATTGCCAT  >  CP000730/39241‑39512

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: