Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 852,632 C→T 18.9% A76V (GCG→GTG)  clpP_1 → ATP‑dependent Clp protease proteolytic subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE852,6320CT18.9% 81.4 / 14.3 37A76V (GCG→GTG) clpP_1ATP‑dependent Clp protease proteolytic subunit
Reads supporting (aligned to +/- strand):  ref base C (14/16);  new base T (3/4);  total (17/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.39e-01

TATTATGTTAGGTTCACAAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGTTACCAAATGCAGAAGTAATGATTC  >  USA300TCH1516_ALE/852492‑852772
                                                                                                                                            |                                                                                                                                            
tattatGTTAGGTTCACAAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGc                                                                                                                                              >  1:71042/1‑141 (MQ=255)
tattatGTTAGGTTCACAAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGc                                                                                                                                              >  1:24263/1‑141 (MQ=255)
        tAGGTTCACAAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGTGATTTATg                                                                                                                                      <  2:125710/141‑1 (MQ=255)
            ttCACAAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATAc                                                                                                                                  <  1:238832/141‑1 (MQ=255)
             tCACAAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACa                                                                                                                                 >  2:356061/1‑141 (MQ=255)
                caAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGTGATTTATGATACAAtt                                                                                                                              <  2:156069/141‑1 (MQ=255)
                caAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAAtt                                                                                                                              >  2:241186/1‑141 (MQ=255)
                 aaaTTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTc                                                                                                                             >  2:97440/1‑141 (MQ=255)
                      gatgaCAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAacac                                                                                                                        <  1:324619/141‑1 (MQ=255)
                                  gCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGAt                                                                                                            >  1:301756/1‑141 (MQ=255)
                                        tCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCaa                                                                                                      <  1:308628/141‑1 (MQ=255)
                                          aaTCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAAc                                                                                                    <  1:299013/141‑1 (MQ=255)
                                           aTCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGTGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACa                                                                                                   >  1:349269/1‑141 (MQ=255)
                                           aTCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACa                                                                                                   >  2:177260/1‑141 (MQ=255)
                                           aTCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACa                                                                                                   <  2:256816/141‑1 (MQ=255)
                                                     aGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGTGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCg                                                                                         >  1:182607/1‑141 (MQ=255)
                                                          ttattCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATg                                                                                    >  1:326270/1‑141 (MQ=255)
                                                             ttCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGTGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCt                                                                                 <  2:97379/141‑1 (MQ=255)
                                                                   cAAGCGCAAGACTCAGAGAAAGATATTTATTTATACCTTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCa                                                                           <  1:282823/141‑1 (MQ=255)
                                                                     aGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAAt                                                                         >  1:43518/1‑141 (MQ=255)
                                                                         cAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGa                                                                     <  2:41794/141‑1 (MQ=255)
                                                                           aGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATc                                                                   >  2:334515/1‑141 (MQ=255)
                                                                                    gaAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGNATGGCTGCATCANTGGGATCATTCttatt                                                          <  1:330105/141‑1 (MQ=255)
                                                                                      aaGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGTGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTag                                                        <  1:267721/141‑1 (MQ=255)
                                                                                        gATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTagca                                                      <  1:177260/141‑1 (MQ=255)
                                                                                                      cATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAgg                                        <  1:86637/141‑1 (MQ=255)
                                                                                                       aTTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGTGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGt                                       >  2:290335/1‑141 (MQ=255)
                                                                                                       aTTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGt                                       <  1:51297/141‑1 (MQ=255)
                                                                                                       aTTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGt                                       <  1:51267/141‑1 (MQ=255)
                                                                                                        ttAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTa                                      <  2:231539/141‑1 (MQ=255)
                                                                                                         tAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTaa                                     >  1:59213/1‑141 (MQ=255)
                                                                                                            ttCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACg                                  >  1:77727/1‑141 (MQ=255)
                                                                                                               aCCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGttt                               <  1:241811/141‑1 (MQ=255)
                                                                                                                ccAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTc                              >  1:140823/1‑141 (MQ=255)
                                                                                                                    gTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGt                          >  1:121143/1‑141 (MQ=255)
                                                                                                                      ggAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGTTa                        <  1:85933/141‑1 (MQ=255)
                                                                                                                       gAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGTTAc                       >  2:330391/1‑141 (MQ=255)
                                                                                                                         aGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGTTACCa                     <  2:289253/141‑1 (MQ=255)
                                                                                                                                       ttttGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGAAGATGCTGCAAAAGGTAACCGTTTAGCGTTACCAAATGAAGAAGTAAt       >  1:171413/1‑141 (MQ=255)
                                                                                                                                            cGATTTATGATACAATTCCACACCTTAAACCTGCTGTTCAAACTATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGTTACCAAATGCAGAAGTAATGATTc  <  1:356061/141‑1 (MQ=255)
                                                                                                                                            cGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGTTACCAAATGCAGAAGTAATGATTc  <  2:10021/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                            
TATTATGTTAGGTTCACAAATTGATGACAACGTAGCAAATTCAATCGTATCACAGTTATTATTCTTACAAGCGCAAGACTCAGAGAAAGATATTTATTTATACATTAATTCACCAGGTGGAAGTGTAACAGCTGGTTTTGCGATTTATGATACAATTCAACACATTAAACCTGATGTTCAAACAATTTGTATCGGTATGGCTGCATCAATGGGATCATTCTTATTAGCAGCTGGTGCAAAAGGTAAACGTTTCGCGTTACCAAATGCAGAAGTAATGATTC  >  USA300TCH1516_ALE/852492‑852772

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