Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 4,272,855 A→G L50P (CTC→CCC)  espX5 ← T3SS effector pentapeptide repeat protein EspX5

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,272,8550AG90.3% 88.1 / 0.6 31L50P (CTC→CCC) espX5T3SS effector pentapeptide repeat protein EspX5
Reads supporting (aligned to +/- strand):  ref base A (2/1);  new base G (13/15);  total (15/16)
Fisher's exact test for biased strand distribution p-value = 6.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.48e-01

TATATCTATAAAATATTTATGTATTTTCCTGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGAGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTAAA  >  NZ_CP009273/4272719‑4272989
                                                                                                                                        |                                                                                                                                      
tataTCTATAAAATATTTATGTATTTTCCTGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAgggg                                                                                                                                      >  2:731676/1‑139 (MQ=255)
         aaaaTATTTATGTATTTTCCTGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTg                                                                                                                             >  2:396665/1‑139 (MQ=255)
         aaaaTATTTATGTATTTTCCTGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTg                                                                                                                             >  2:638854/1‑139 (MQ=255)
               tttATGTATTTTCCTGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAAt                                                                                                                        >  2:119905/1‑138 (MQ=255)
                   tGTATTTTCCTGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACg                                                                                                                   <  1:731676/139‑1 (MQ=255)
                             tGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTat                                                                                                          >  2:846004/1‑138 (MQ=255)
                               tCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTatgat                                                                                                       <  2:377417/139‑1 (MQ=255)
                               tCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTatgat                                                                                                       <  2:211695/139‑1 (MQ=255)
                               tCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTatgat                                                                                                       <  1:119905/139‑1 (MQ=255)
                               tCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTatgat                                                                                                       >  2:1186921/1‑139 (MQ=255)
                                         tcGTGATTTTTCCTGAGGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGAGGGCTTTCTTGTCAATTAACGTGTTTTTATGATGTTTGCTGt                                                                                              >  2:687829/1‑138 (MQ=255)
                                                  ttCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTg                                                                                     <  2:912630/138‑1 (MQ=255)
                                                         tGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGtt                                                                             <  1:911194/139‑1 (MQ=255)
                                                         tGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGtt                                                                             <  2:374811/139‑1 (MQ=255)
                                                          ggTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGttt                                                                            >  2:718625/1‑139 (MQ=255)
                                                                   tCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTAt                                                                   >  2:626346/1‑139 (MQ=255)
                                                                    cATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTAtg                                                                  >  1:577384/1‑139 (MQ=255)
                                                                        aaTTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGAt                                                              <  2:168551/139‑1 (MQ=255)
                                                                           tCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGAt                                                              <  1:374579/136‑1 (MQ=255)
                                                                           tCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGAt                                                              >  2:374579/1‑136 (MQ=255)
                                                                           tCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGa                                                           >  2:721374/1‑139 (MQ=255)
                                                                               ttCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGAGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGAc                                                          <  1:687829/136‑1 (MQ=255)
                                                                                  aTTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGa                                                    <  1:361741/139‑1 (MQ=255)
                                                                                           aTCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGt                                           <  2:362448/139‑1 (MQ=255)
                                                                                                    aTCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTaa                                  >  1:1000693/1‑139 (MQ=255)
                                                                                                     tCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCt                                                                         <  2:996185/99‑1 (MQ=255)
                                                                                                     tCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCt                                                                         >  1:996185/1‑99 (MQ=255)
                                                                                                     tCACTTTTTCATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAAt                                 <  2:81198/139‑1 (MQ=255)
                                                                                                           tttCATGATCATCCATTTTGAAAAGAGAGAGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGc                            >  2:1285269/1‑138 (MQ=255)
                                                                                                              cATGATCATCCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCaaa                         <  1:776808/138‑1 (MQ=255)
                                                                                                                  atcatcCATTTTGAAAAGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAggg                    <  1:824591/139‑1 (MQ=255)
                                                                                                                               aaaaGAGAGGGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACAtattat       >  2:841740/1‑139 (MQ=255)
                                                                                                                                  agagagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTa    <  2:379838/139‑1 (MQ=255)
                                                                                                                                  agagagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTa    <  1:721374/139‑1 (MQ=255)
                                                                                                                                  agagagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTa    <  1:638854/139‑1 (MQ=255)
                                                                                                                                  agagagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTa    <  1:396665/139‑1 (MQ=255)
                                                                                                                                  agagagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTa    <  2:951978/139‑1 (MQ=255)
                                                                                                                                  agagagagGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTa    <  2:802750/139‑1 (MQ=255)
                                                                                                                                    agagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTaaa  <  1:1186921/139‑1 (MQ=255)
                                                                                                                                     gagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTg                                                                                                  >  2:1029837/1‑42 (MQ=255)
                                                                                                                                     gagggGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTg                                                                                                  <  1:1029837/42‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                      
TATATCTATAAAATATTTATGTATTTTCCTGTCCGTTTCTTTCGTGATTTTTCCTGATGGTAAACTATCATAAATTCTTTTCATTTTCTGAATCAAGCCTATCACTTTTTCATGATCATCCATTTTGAAAAGAGAGAGGGCTTTATTGTCAATTAACGTGTTTTTATGATGTTTGCTGTAATTATCTGATTTTGTTTTCTTTGTATGTGATGGACTTGTGACAGAGTGGTTATCGTTAATCAGGCAAAGAGGGAAAAACATATTATTTAAA  >  NZ_CP009273/4272719‑4272989

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑