Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,027,432 G→A 9.7% A172V (GCT→GTT)  vraS ← Sensor protein VraS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,027,4320GA 9.7% 115.1 / 2.4 41A172V (GCT→GTT) vraSSensor protein VraS
Reads supporting (aligned to +/- strand):  ref base G (16/21);  new base A (2/2);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

CACCTAAAGATTTGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTT  >  USA300TCH1516_ALE/2027292‑2027570
                                                                                                                                            |                                                                                                                                          
aaCCTAAAGATTTGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAATGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTCATGGTGGTTCTAACTTCGTTTCTTTtatag                                                                                                                                            <  2:405366/140‑1 (MQ=255)
 aCCTAAAGATTTGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTgatagc                                                                                                                                           >  1:81646/1‑141 (MQ=255)
     aaaGATTTGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTgatagcagat                                                                                                                                       <  2:410999/141‑1 (MQ=255)
        gATTTGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTgatagcagatagc                                                                                                                                    <  1:397937/141‑1 (MQ=255)
         aTTTGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTgatagcagatagca                                                                                                                                   <  1:50458/141‑1 (MQ=255)
           ttGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGcatc                                                                                                                                 <  2:466208/141‑1 (MQ=255)
             gTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCCTTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGCTGGTCTAATGGTGGTTCTAACTTGGTTTCTTTGATAACAGATAGcatcat                                                                                                                               >  1:261317/1‑141 (MQ=255)
             gTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGcatcat                                                                                                                               >  1:18276/1‑141 (MQ=255)
                ttttAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAGTCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACt                                                                                                                            <  1:373199/141‑1 (MQ=255)
                  ttAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTg                                                                                                                          >  1:39149/1‑141 (MQ=255)
                  ttAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCAGTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTg                                                                                                                          <  2:516663/141‑1 (MQ=255)
                    aaaCCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGcc                                                                                                                        >  1:399645/1‑141 (MQ=255)
                      aCCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCGTTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGc                                                                                                                      <  2:555636/141‑1 (MQ=255)
                                  tAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGGATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTg                                                                                                          >  1:267757/1‑141 (MQ=255)
                                   aaaTGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGa                                                                                                         >  1:76799/1‑141 (MQ=255)
                                     aTGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTGGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATAATTGAAGCAAAAAGTTGCTGACt                                                                                                       <  2:482659/141‑1 (MQ=255)
                                       gTAACAGCAAAGCACGCATTTCTAACTGCTAATCTCGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTTGTTCTAACTTCTCTTCTCTGATAGCAGATAGCCTCATACTTGCCGCAAAAAGTTGCTGCCTac                                                                                                     <  1:293948/141‑2 (MQ=255)
                                       gTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTaa                                                                                                     <  1:438699/141‑1 (MQ=255)
                                       gTAACAGCAAAGCACGAATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTaa                                                                                                     >  1:330855/1‑141 (MQ=255)
                                          aCAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAg                                                                                                  <  2:254622/141‑1 (MQ=255)
                                             gCAAAGCACGCATTTCTAACGGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATGCTTGCCGCAAAAAGTTGCTGTCTAACAGAAt                                                                                               <  2:335582/141‑1 (MQ=255)
                                              cAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATc                                                                                              <  1:161031/141‑1 (MQ=255)
                                                   cACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGaa                                                                                         <  1:169427/141‑1 (MQ=255)
                                                     cGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGt                                                                                       >  1:97484/1‑141 (MQ=255)
                                                       cATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGCTAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGGtc                                                                                     >  1:378261/1‑141 (MQ=255)
                                                        tcttCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTtct                                                                                    <  2:621944/139‑1 (MQ=255)
                                                           tCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGt                                                                                 <  2:608485/141‑1 (MQ=255)
                                                           tCTAACGGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGt                                                                                 <  2:83637/141‑1 (MQ=255)
                                                              aaCTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCt                                                                              <  1:49015/141‑1 (MQ=255)
                                                                   cGAATCTTGAAGCATTTGCTCTACAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGGTGCTGACGAACAGAATCGTGAAGTTCTCGTGCTAGTCt                                                                         <  2:266977/141‑1 (MQ=255)
                                                                                aTTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTCATAGCAGATAGCATCATACTTGCCGCAAAAAGTGGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCt                                                            >  1:299737/1‑141 (MQ=255)
                                                                                            aTAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAACAGATAGCATCATTCTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCttt                                                <  2:11240/141‑1 (MQ=255)
                                                                                            aTAGGAATTTGTTCGTCTAATGGGGGTTCTAACTTCGTTTCTTTGATAACAGATAGCATCAAAATTGACGAAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCttt                                                <  2:182367/141‑1 (MQ=255)
                                                                                             tAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCtttt                                               <  2:206939/141‑1 (MQ=255)
                                                                                                         ggTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCAcat                                   >  1:172328/1‑141 (MQ=255)
                                                                                                         ggTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATAATACTTGCCGCAAAAAGTTGCTGACTAACACAATCGTGCAGTTCTCGTACTAATCTTAGTCGTTCATCTTCAATAATCTTTTTAACTTTCAcat                                   <  2:132559/141‑1 (MQ=255)
                                                                                                         ggTCTAATGGTGGTTCTAACTTCGGTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCAcat                                   <  2:396982/141‑1 (MQ=255)
                                                                                                                  gtggtTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGGTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTagtgt                          >  2:147845/1‑137 (MQ=255)
                                                                                                                   tggtTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCCTTAAtatt                         >  2:378509/1‑141 (MQ=255)
                                                                                                                           aCTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAAtttt                 >  1:633813/1‑141 (MQ=255)
                                                                                                                           aCTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAAtttt                 <  1:625685/141‑1 (MQ=255)
                                                                                                                             ttCGTTTCTTTGATCACAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCAAGTCTTTGACGTACATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCa               >  2:455552/1‑141 (MQ=255)
                                                                                                                                    cTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTa        >  2:310576/1‑141 (MQ=255)
                                                                                                                                      ttGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTaat      >  2:111166/1‑140 (MQ=255)
                                                                                                                                      ttGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTGTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAg      >  1:52979/1‑141 (MQ=255)
                                                                                                                                       tGATAGCAGAGAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGt     <  2:81646/141‑1 (MQ=255)
                                                                                                                                        gatagcagatagccTCATAATTGCCGCATAAAGTTGCTGACTAACAGAACCGTGAAGTTCTCGTGTTAGTCTTTGATGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTTAGtt    <  1:528920/141‑1 (MQ=255)
                                                                                                                                          tagcagatagcaTCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGtttt  >  2:33722/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                          
CACCTAAAGATTTGTCTTTTAAACCAAGCGGTCTTAAATGTAACAGCAAAGCACGCATTTCTAACTGCGAATCTTGAACCATTTTCTCTAAAATAGGAATTTGTTGGTCTAATGGTGGTTCTAACTTCGTTTCTTTGATAGCAGATAGCATCATACTTGCCGCAAAAAGTTGCTGACTAACAGAATCGTGAAGTTCTCGTGCTAGTCTTTGACGTTCATCTTCAATAATCTTTTTAACTTTCACATCATTAATATTATAATTTTCATTGGTTAAGTTTT  >  USA300TCH1516_ALE/2027292‑2027570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑