Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,217,669 T→A 10.1% *71K (TAA→AAA)  USA300HOU_1144 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,217,6690TA10.1% 143.4 / 2.6 59*71K (TAA→AAA) USA300HOU_1144hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (24/28);  new base A (3/4);  total (27/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAATCTATCTAGTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATAC  >  CP000730/1217535‑1217807
                                                                                                                                      |                                                                                                                                          
ccAATCTATCTAGTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTCAACATGTAAAGGATATATTACGTCAACAAGAACAAATTTaaaaa                                                                                                                                       <  1:462513/140‑1 (MQ=255)
 cAATCTATCTAGTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGTTATATTACGTAAACAAGAACAAATTTAAAAAc                                                                                                                                      >  2:263603/1‑140 (MQ=255)
 cAATCTATCTAGTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAAc                                                                                                                                      >  2:330349/1‑140 (MQ=255)
 cAATCTATCTAGTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAAc                                                                                                                                      >  2:511989/1‑140 (MQ=255)
 cAATCTATCTAGTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACAAATAAAAAATAAAACAACTATAAATCATAATGATGATTTATTAAACCATATAACGGCTATAATACGTAAACAAGAACAAATTAAAAAAc                                                                                                                                      >  2:589534/1‑140 (MQ=255)
 cAATCTATCTAGTAGTCACGATGTCGACGAAAGATCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAACTTTAAAAAc                                                                                                                                      <  1:557974/140‑1 (MQ=255)
  aaTCTATCTAGTAGTAACGATGTCGACGAAAGATCAACAAAACAAAAACATAAAAAAAATAAAACAACTATAGATCAAAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAAATTAAAAACa                                                                                                                                     <  2:749140/140‑1 (MQ=255)
          tagtagTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCt                                                                                                                             >  2:565973/1‑140 (MQ=255)
             tagtCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCtata                                                                                                                          >  2:89272/1‑140 (MQ=255)
             tagtCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAAAAAAAAAGCtaaa                                                                                                                          >  2:212855/1‑138 (MQ=255)
                   cGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGttt                                                                                                                    >  2:328582/1‑140 (MQ=255)
                   cGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGttt                                                                                                                    >  2:339617/1‑140 (MQ=255)
                    gaggTCGACGAAAGTTCAACAAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACAGTTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTa                                                                                                                   <  1:673511/137‑1 (MQ=255)
                     aTGTCGACGAAAGTTCAAAGTAGCAAAAAAATATAAAAAATTAAACAACTATAGCTAATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTAAAAAACAAAAAAGCtaagatagttaa                                                                                                                  >  2:86065/1‑130 (MQ=255)
                         ctaaaaaaGTTCAAAGAAGCAAAAACATATAAAAAATAAAACAACGATAGAACATAATGATGATTTATTTAAACAAATAAAGGATATATTACGTAAACAAGAACAAAAAAAAAAAAAAAAAAGCTATAGTGTTTAATATc                                                                                                              <  2:643841/135‑1 (MQ=255)
                         cgactaAAGTTCAACGAATAAAAAACATATAAAAAATAAAACAACTATAAATCATAATGATGATTTATTTAAACATTTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATc                                                                                                              <  2:131196/140‑1 (MQ=255)
                           acgaAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATATATCATAATGATGATTTATTTAAACATGTAAAGAATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATACTGTTTAATATCAg                                                                                                            >  1:399576/1‑140 (MQ=255)
                                   tCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGgctgct                                                                                                    >  1:642218/1‑140 (MQ=255)
                                   tCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGgctgct                                                                                                    >  2:90854/1‑140 (MQ=255)
                                   tCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAAAAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGgctgct                                                                                                    >  1:154827/1‑140 (MQ=255)
                                    cAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAACTATAGTGTTTAATATCAGGGGATGAtt                                                                                                   >  1:737026/1‑140 (MQ=255)
                                              aaaaCATTTAAAAAATAAAACAATTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATcc                                                                                         <  1:160509/140‑1 (MQ=255)
                                              aaaaCATAAAAAAAATAAAAGAACTAAAGATCAAAATGATGAATTAATTAAACAAAAAAAGGATATATTACGTAAACAAGAACAAAAAAAAAAAAAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATcc                                                                                         <  2:172829/140‑1 (MQ=255)
                                                       aaaaaaTAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTAc                                                                                <  1:586504/140‑1 (MQ=255)
                                                             tAAAATAACTATAGAGAATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAacac                                                                          <  2:399576/140‑1 (MQ=255)
                                                             tAAAACAACTATAGATTATAATGATGATTTATTTAAACATGGAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAacac                                                                          <  2:236489/140‑1 (MQ=255)
                                                             tAAAACAACTATAGATCATATTGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAacac                                                                          <  1:237810/140‑1 (MQ=255)
                                                             tAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATCGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAacac                                                                          <  1:151960/140‑1 (MQ=255)
                                                              aaaaCAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACt                                                                         >  1:643424/1‑140 (MQ=255)
                                                              aaaaCAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACt                                                                         <  1:589534/140‑1 (MQ=255)
                                                                 acaacTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACtata                                                                      >  1:432309/1‑140 (MQ=255)
                                                                 acaacTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAAAACtata                                                                      >  1:617417/1‑140 (MQ=255)
                                                                          gATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTttatt                                                             >  1:286573/1‑140 (MQ=255)
                                                                          gATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTAAAGCTTttatt                                                             >  1:115994/1‑140 (MQ=255)
                                                                           caaaTAATGATGATATATATAAATATGTAAAGAATATATTACTTAAACAAGAAAAAATTAAAAAAAAAAAAAGCTATAGTGTTTAATATCAGGGGGGGCTTAACCGCATCCGAATATTACTTTCATTATAGCTTttaaaa                                                            <  2:313185/137‑4 (MQ=255)
                                                                             cacaaggatgatTTATTTAAACATGTCAAGGATATATTACGTAAACCAGAACAAATTTAAAAACAAAAAAGCTGTAGTTTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATtata                                                          <  1:440105/134‑1 (MQ=255)
                                                                             cATAATGATGATTTATTTAAACATGTAAAGGATATACTACGAAAACAAGAAAAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATtata                                                          <  2:174323/140‑1 (MQ=255)
                                                                             cATAAGGATCATTTATTTAAACATGTAAATGATATATTACGTAAACAACAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCATGTGCTGCTTAACCGCATCCGAATATTACAAACACTATAGTTTTTATtata                                                          <  2:68358/140‑1 (MQ=255)
                                                                                aaTTATGATTTATTTAAACATGTAAAGGATATATTACGTAAACACGAACAACTTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATaa                                                       <  1:268978/140‑1 (MQ=255)
                                                                                aaTGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATaa                                                       <  1:104832/140‑1 (MQ=255)
                                                                                   gatgatTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATaaaaa                                                    >  1:489677/1‑140 (MQ=255)
                                                                                              taAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGTCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCg                                         <  1:478719/140‑1 (MQ=255)
                                                                                                  cATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATa                                     <  2:279458/140‑1 (MQ=255)
                                                                                                       aaaGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGTGGCTGCTTAACCGCATCCGAATATTACAACCACTATAGCTTTTATTATATAAAAACTTTATAAGCGGATAGTTaa                                >  2:263999/1‑140 (MQ=255)
                                                                                                             tatatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTttat                          >  1:117981/1‑140 (MQ=255)
                                                                                                             tatatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGAGGGAAAATAACTttat                          >  2:760461/1‑140 (MQ=255)
                                                                                                              atatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGGGGATAATTAACTttatt                         <  2:154827/140‑1 (MQ=255)
                                                                                                              atatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTttatt                         <  2:642218/140‑1 (MQ=255)
                                                                                                              atatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTttatt                         <  1:645027/140‑1 (MQ=255)
                                                                                                              atatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCCGATAATTAACTttatt                         <  2:699383/140‑1 (MQ=255)
                                                                                                                   aCGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTACCTTTATTAAAAt                    <  2:466045/140‑1 (MQ=255)
                                                                                                                         aCAAAACCAAATTAAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGTCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCATAAAATTAACTTTATTAAAATccaacc              >  2:343225/1‑140 (MQ=255)
                                                                                                                           aaGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTGATTATATAAAAAATTTATTAGCGGAAAATTAACTTTATTAAAAAcaaaccaa            >  1:61207/1‑140 (MQ=255)
                                                                                                                            aGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAAt           >  1:167050/1‑140 (MQ=255)
                                                                                                                              aaCAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTCAAATCCAACCAATTa         <  1:565973/140‑1 (MQ=255)
                                                                                                                              aaCAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTa         <  1:289424/140‑1 (MQ=255)
                                                                                                                              aaCAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTa         <  1:90854/140‑1 (MQ=255)
                                                                                                                                  aaTTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATGAAAATCCAACCAATTAAGaa     <  1:459992/140‑1 (MQ=255)
                                                                                                                                  aaTTAAAAAAAAAAAAAGCAAAAGTATTTAATATCACGGCCTGATTAACCACATCAGAATATTACAAACACTATAGCTATAAAAAAAAAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGaa     <  2:367473/140‑1 (MQ=255)
                                                                                                                                     ttAAAAACAAAAAAGCTATCGTGTTTAATATCTGGGGCTGCTTAACCGCTTCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATAc  <  1:108872/140‑1 (MQ=255)
                                                                                                                                     ttAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATAc  <  1:201304/140‑1 (MQ=255)
                                                                                                                                     ttAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATAc  <  1:451047/140‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                          
CCAATCTATCTAGTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATAC  >  CP000730/1217535‑1217807

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: ‑