Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000731 25,663 Δ1 bp 100% coding (316/333 nt) USA300HOU_pUSA300HOUMR0031 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073125,6630A.96.2% 223.1 / 1.0 53coding (316/333 nt)USA300HOU_pUSA300HOUMR0031hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base . (28/23);  total (29/24)
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
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.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

ATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAG  >  CP000731/25528‑25791
                                                                                                                                       |                                                                                                                                
atGTTATTTACACTATTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATTCTGTTTGATTACTATACTACAAATa                                                                                                                                  <  1:105217/136‑1 (MQ=255)
    tATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaaa                                                                                                                              <  1:32845/136‑1 (MQ=255)
     aTTTACACTAGTGATTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTATTATACTACAAATaaaaaa                                                                                                                             >  2:59462/1‑136 (MQ=255)
      tttACACTTGTGCTTAAATTTACAGATTTGTCACCAAGTATTGAAAGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaaaat                                                                                                                            >  1:9458/1‑135 (MQ=255)
           acTAGTGCTTAAATTTACAGGTTTATCACCAAATATTGAAGGAACTTGATTTTCTCAATATAAAGCACAAAGCGTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACa                                                                                                                      >  1:61297/1‑136 (MQ=255)
              aGTGCTTAAATTTACATGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTATCACTATTTCTTATGCTGTTTAATTTCTATACTACAAAT‑AAAAAATATACATCt                                                                                                                   <  1:104126/136‑1 (MQ=255)
                   ttAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGTACTATTTCTTATGCTGTTTAATTACTATCCTACATAT‑AAAAAATATACATCTAAAgg                                                                                                              >  2:103007/1‑136 (MQ=255)
                   ttAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTCTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAgg                                                                                                              >  2:67886/1‑136 (MQ=255)
                         ttACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAAt                                                                                                        >  2:147063/1‑136 (MQ=255)
                             aGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTATTTAATTACTATACTAAAAAT‑AACAAATATAAAACTAAAAGTTAAATTAAt                                                                                                    >  2:41418/1‑136 (MQ=255)
                              ggTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATAATCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATg                                                                                                   >  2:94500/1‑136 (MQ=255)
                                 ttttCACCAAGTATTGAAGGATCTTAATTATAACAAAAAACAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaaa                                                                                                >  1:23945/4‑136 (MQ=255)
                                 ttGTCACTAAGTATTGAAGGATCTTGGTTTTTTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGaaa                                                                                                <  2:46972/136‑1 (MQ=255)
                                   gTCACAAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTAATTCTTATGCTTTTTAATTACTATACTATAAAT‑AAAAAATATACATTTAAAAGTTAAATTAATGaaaaa                                                                                              <  1:18816/136‑1 (MQ=255)
                                      aCCAAGTATTGAAGGATCTTGGTTTTCTCAATGTCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAg                                                                                           <  1:20803/136‑1 (MQ=255)
                                         aaGTATTTAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAAt                                                                                        <  1:77963/136‑1 (MQ=255)
                                         aaGTATTGAAGGATCATGATATTCTCAAAAACCAAAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAAt                                                                                        >  1:89499/1‑136 (MQ=255)
                                          aGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAACTATACATCTAACAGTTAAATTAATTAAAAAAAAAAtt                                                                                       >  2:143351/1‑136 (MQ=255)
                                               tGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATATATCTAAAGGTTAAATTAATGAAAAATAGAATgagaga                                                                                  <  1:132499/136‑1 (MQ=255)
                                                     aTCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAg                                                                            >  1:94616/1‑136 (MQ=255)
                                                       cTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGaa                                                                          >  2:69917/1‑136 (MQ=255)
                                                          ggTTGTCTCAATATGCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAAc                                                                       <  2:13987/136‑1 (MQ=255)
                                                           gTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACa                                                                      <  1:142672/136‑1 (MQ=255)
                                                              ttCTAAATATACAGAAATTTTCTTTATAATTATAGAACTATTTATTATGCTGTTTAATTACTATACTAAAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACaaaa                                                                   <  2:31068/136‑1 (MQ=255)
                                                                    atatCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAAt                                                             <  1:156014/136‑1 (MQ=255)
                                                                     tatCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAAtt                                                            >  1:65364/1‑136 (MQ=255)
                                                                      atCCAGACATTTTCTTTATAATTGTAAAACTAATACTAATACAATTTAATAACTAAACTACAAAT‑AAAAAATATACATCAAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAAttt                                                           >  1:26289/1‑136 (MQ=255)
                                                                         cAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGATGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGCAAtttata                                                        >  2:122040/1‑133 (MQ=255)
                                                                               ttttCTTTATAATTGTAGCAATATTTCTTATGCTGTTTAATTACTATAATACAAA‑AAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGaaa                                                  <  2:1876/136‑1 (MQ=255)
                                                                                tttCTTTAGAATTGTAGCACTAATTCTTATGCTGTATAATGACTATACTAGAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAAc                                                 <  2:147027/136‑1 (MQ=255)
                                                                                   ttttATAATTGTAGCACTATTTCTTATGCTGTTTAATTAATATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACttt                                              <  2:7762/135‑1 (MQ=255)
                                                                                    tttATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACtata                                             >  2:98813/1‑136 (MQ=255)
                                                                                     ttATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGTATTAGAGAATTTAGTATTTAAAAAGGAATTTCTCAAGAAACTTTaa                                            <  1:141934/136‑1 (MQ=255)
                                                                                     ttATAATTGTAGCACTAATCATTATAATCTTTCATTACTATACTACAAATAAAAAAA‑ATAAATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATCTAGAAAACAAAAAGTATTTTCTCAAGAAACtttga                                            >  2:58437/1‑134 (MQ=255)
                                                                                      tataATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAg                                           >  1:79105/1‑136 (MQ=255)
                                                                                       ataATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATCTAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGt                                          >  2:126322/1‑136 (MQ=255)
                                                                                          aTTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTaaa                                       <  1:41418/136‑1 (MQ=255)
                                                                                             gTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAATTTTTTTTTTCAAGAAACTTTaagaaaagaa                                    <  1:164/136‑1 (MQ=255)
                                                                                             gTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGaa                                    >  2:61098/1‑136 (MQ=255)
                                                                                                  aCTATTTCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTaaa                               >  1:93057/1‑136 (MQ=255)
                                                                                                      tttCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAATCTTTAAGTAAAGAATTAAAAgtg                           <  1:147063/136‑1 (MQ=255)
                                                                                                       ttCTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAgtgt                          >  1:52071/1‑136 (MQ=255)
                                                                                                         cTTATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTCAAGAATAAAAAATGTCt                        >  2:33196/1‑136 (MQ=255)
                                                                                                         cTTATGCTGTTTAATTACTATAATACAAAT‑AAAAAATATACAACTAAAGGTTAAATTAATGAAAAATAGAATAATATAAAAGAGAAAATCTATATGATTTTCTCAAGAATCTTTAAGTAAAGAATTAAAAGTGTCt                        <  1:163188/136‑1 (MQ=255)
                                                                                                           tATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAg                      >  1:20433/1‑136 (MQ=255)
                                                                                                           tATGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATATAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAAAGAAAAGTCTCTaa                      >  2:101602/1‑135 (MQ=255)
                                                                                                            aTGCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAgg                     >  1:71200/1‑136 (MQ=255)
                                                                                                              gCTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTCACTAGGCa                   >  2:108967/1‑136 (MQ=255)
                                                                                                               cTGTTTAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCaa                  >  1:42905/1‑136 (MQ=255)
                                                                                                                   ttAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAATCTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTa              <  1:39846/136‑1 (MQ=255)
                                                                                                                   ttAATTACTATAATACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCCCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTa              <  2:62499/136‑1 (MQ=255)
                                                                                                                   ttAATTACGATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTa              <  2:115066/136‑1 (MQ=255)
                                                                                                                    tAATTACTATACTACAAAT‑AAAAAATATACATCTAAAGGATAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTAt             >  1:8585/1‑136 (MQ=255)
                                                                                                                     aaTTACTATACTACAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTAtt            <  1:717/136‑1 (MQ=255)
                                                                                                                           tatactaCAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATgaa      >  2:26349/1‑134 (MQ=255)
                                                                                                                             aactaaAAAT‑AAAAAATATACATATAAAAGTTAAATTAATCAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAATTAAAGAATTAAAAGTGTCTATGCAAACTATTAATGCAAt    <  1:7641/135‑1 (MQ=255)
                                                                                                                               atacAAAT‑AAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAAAATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAg  <  1:129651/135‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                
ATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAG  >  CP000731/25528‑25791

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: ‑