Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,298,108 T→A 100% intergenic (+4/‑232) pnp → / → USA300HOU_1207 polyribonucleotide nucleotidyltransferase/beta‑lactamase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,298,1080TA100.0% 107.8 / ‑6.5 37intergenic (+4/‑232)pnp/USA300HOU_1207polyribonucleotide nucleotidyltransferase/beta‑lactamase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  major base A (17/18);  minor base G (1/0);  total (18/19)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAT  >  CP000730/1297972‑1298238
                                                                                                                                        |                                                                                                                                  
ttCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGATACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATaaa                                                                                                                                >  1:473706/1‑141 (MQ=255)
ttCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGATACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATaaa                                                                                                                                >  1:473872/1‑141 (MQ=255)
          tCAAAAAATAGAATCGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgac                                                                                                                      >  1:608632/1‑141 (MQ=255)
            aaaaaaTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgacga                                                                                                                    <  1:401312/141‑1 (MQ=255)
            aaaaaaTAAAATTGAAAAAGTGGAAGATGTATTAAAAAGCGGTAACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAAGTCGATGAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgacga                                                                                                                    <  2:68412/141‑1 (MQ=255)
              aaaaTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATGGATAAACAAGATCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATGTAAAGTACTATGACGACa                                                                                                                  >  2:345432/1‑141 (MQ=255)
                 aTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATg                                                                                                               <  1:479356/141‑1 (MQ=255)
                 aTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATg                                                                                                               <  1:394992/141‑1 (MQ=255)
                      aTTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGATAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAAAAGAATAATATATAAAGTCATCTGACAACAATGTATCg                                                                                                          >  2:319835/1‑141 (MQ=255)
                           aaaaGTGGAAGATGTATTAAAAATCGGTGACACAATTGAACTTAAGACTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCAtg                                                                                                     >  2:432254/1‑141 (MQ=255)
                                 ggAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGAttt                                                                                               >  1:51176/1‑141 (MQ=255)
                                           ttAAAAATCGGTGACAAAATTAAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCa                                                                                     >  1:341913/1‑141 (MQ=255)
                                             aaaaaTCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACt                                                                                   <  2:661483/141‑1 (MQ=255)
                                             aaaaaTCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACt                                                                                   <  2:131621/141‑1 (MQ=255)
                                               aaaTCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACttt                                                                                 <  2:87551/141‑1 (MQ=255)
                                                   cGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATTCCACTTTTTAc                                                                             >  2:614829/1‑141 (MQ=255)
                                                    ggTGACACAATTAAAGTTAAGATTACTGAAAATGATAAACAAGGTCGAGTAAAAGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACg                                                                            >  2:640831/1‑141 (MQ=255)
                                                     gTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGa                                                                           >  2:499024/1‑141 (MQ=255)
                                                       gACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAg                                                                         >  2:352184/1‑141 (MQ=255)
                                                               tGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGt                                                                 <  2:51176/141‑1 (MQ=255)
                                                                 aaGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGttt                                                               <  1:174495/141‑1 (MQ=255)
                                                                                  aTTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGa                                              <  1:583927/141‑1 (MQ=255)
                                                                                         aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACAtttt                                       <  1:587699/141‑1 (MQ=255)
                                                                                             aGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTaaaa                                   <  1:499024/141‑1 (MQ=255)
                                                                                              ggTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAAc                                  >  2:449216/1‑141 (MQ=255)
                                                                                                tCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTGTTGAATTTGTTGTATTGAACATTTTAAAACGc                                >  1:445604/1‑141 (MQ=255)
                                                                                                      aaaTGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTttatt                          <  2:341913/141‑1 (MQ=255)
                                                                                                            ttCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTtg                    <  1:510936/141‑1 (MQ=255)
                                                                                                            ttCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTtg                    >  1:363836/1‑141 (MQ=255)
                                                                                                              cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTtgtg                  >  1:35383/1‑141 (MQ=255)
                                                                                                                 aTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGc               >  1:200047/1‑141 (MQ=255)
                                                                                                                       cATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACCCTTTATTATTTTTTTTGTAACTGt         >  2:580834/1‑141 (MQ=255)
                                                                                                                        aTTAGAAGAATAATATATAAAGGCATATGACGACAATGTATCGTCATGTGATTTTTTTAGGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAGCGCTTTATTATTTTGTGTGCAACTGtt        <  2:248674/141‑1 (MQ=255)
                                                                                                                          tAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTaa      <  2:505303/141‑1 (MQ=255)
                                                                                                                           aggagaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAAt     <  1:215580/138‑1 (MQ=255)
                                                                                                                              ataataatATAAAAAGTCATAGGACGACAATGTATCGTCATGTGACTTTTTTATGCCACTTTTTACGAAGTCACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAt  <  2:18808/139‑1 (MQ=255)
                                                                                                                              agaaTAATATATAACGTCATATGACGATAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAt  <  2:498911/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                  
TTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAT  >  CP000730/1297972‑1298238

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: