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.98.2% 247.0 / ‑3.3 56coding (316/333 nt)USA300HOU_pUSA300HOUMR0031hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (33/22);  total (33/23)
Fisher's exact test for biased strand distribution p-value = 4.11e-01
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.

TTGTATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAACA  >  CP000731/25524‑25797
                                                                                                                                           |                                                                                                                                      
ttgtatGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaa                                                                                                                                       <  1:61023/141‑1 (MQ=255)
tgttctgttgtTGACACTAGTGCTTAAATTTATAGGTTTGTCACCAAGTATTTAAGGATCTTGGTTTTTTCAATATCCAGAAATTTTCTTTATAATTGTAGTACTATTTATTATGCTTTTTTATTACTATACTACAAATaa                                                                                                                                       <  2:31552/136‑1 (MQ=255)
tagtatGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaa                                                                                                                                       >  1:117847/3‑141 (MQ=255)
    atGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTTTATCACTATTTTTTATGCTGTTTAATTACTATACTACAAATaaaaaa                                                                                                                                   >  1:153568/1‑141 (MQ=255)
       ttATTTACACTATTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATaaaaaatat                                                                                                                                <  1:102824/141‑4 (MQ=255)
         aTTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATAc                                                                                                                             >  1:25464/1‑141 (MQ=255)
          tttACCGTAGTGCTTAGATTTGCAGTTTTGTCACAAAGTCTCGCAGGAGCTTGGTTTTCTCGATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACa                                                                                                                            >  1:95695/1‑141 (MQ=255)
          tttACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACa                                                                                                                            >  2:79589/1‑141 (MQ=255)
           ttACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACAt                                                                                                                           >  1:109923/1‑141 (MQ=255)
           ttACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACAt                                                                                                                           >  2:194450/1‑141 (MQ=255)
           ttACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACAt                                                                                                                           >  1:152863/1‑141 (MQ=255)
              cacTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTa                                                                                                                        >  1:200652/1‑141 (MQ=255)
              cacTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTa                                                                                                                        >  1:67893/1‑141 (MQ=255)
                   gTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGCTCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATCACTATACTACAAATAAAAAATATACATCTAAAGGt                                                                                                                   <  1:192218/141‑1 (MQ=255)
                   gTGATTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGt                                                                                                                   <  2:35396/141‑1 (MQ=255)
                          aaTTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTa                                                                                                            <  1:111880/141‑1 (MQ=255)
                            tttACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTGAATATACAGAAATGTTGTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTGCTATACTACAGATAAAAAAGATACATCGAAAGGTTAAATTact                                                                                                          >  1:54443/1‑139 (MQ=255)
                              aaCAGGTGTGTCACCAAATATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTCTATAATAGTATCATAATTTCTTATGCTGTTTAATTACTAAAATAAAAAAAAAAAATATACATCTAAAGGTTAAATTAATGa                                                                                                        <  2:149931/140‑1 (MQ=255)
                               aCAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACCTCTAAAGGTTAAATTAATGaa                                                                                                       >  1:198551/1‑141 (MQ=255)
                                cAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGTTTAAATTAATGaaa                                                                                                      >  2:114718/1‑141 (MQ=255)
                                cAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGaaa                                                                                                      >  1:176071/1‑141 (MQ=255)
                                cAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGATGTTTAATGACTCTACTACTGATAAAGTTGGTACATCTAACGGTTAAATTCATGaaa                                                                                                      >  1:219967/1‑141 (MQ=255)
                                   gTTTGTCACCAAGTATTGAAGGATCTTTGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAAt                                                                                                   <  1:59229/141‑1 (MQ=255)
                                   gTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAAt                                                                                                   <  1:90070/141‑1 (MQ=255)
                                   gTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAAt                                                                                                   <  1:85144/141‑1 (MQ=255)
                                     ttGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTCAAATTAATGAAAAATaa                                                                                                 >  2:174501/1‑140 (MQ=255)
                                      tGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGa                                                                                                >  1:68795/1‑141 (MQ=255)
                                            cAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTaga                                                                                          >  1:139422/1‑141 (MQ=255)
                                               gTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGaa                                                                                       <  1:196858/141‑1 (MQ=255)
                                                 aTTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAata                                                                                     >  1:163808/1‑141 (MQ=255)
                                                     aaGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGa                                                                                 <  1:3399/141‑1 (MQ=255)
                                                     aaGGATCTTGGTGTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGa                                                                                 <  1:43791/141‑1 (MQ=255)
                                                       ggATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATACAAAATATACATCTAAAGGTTAAACTAATGAAAAATAGAATTAGAGAATATAGaaa                                                                               >  1:34141/1‑141 (MQ=255)
                                                             tGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACaaaa                                                                         >  1:184203/1‑141 (MQ=255)
                                                             tGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACaaaa                                                                         >  1:246498/1‑141 (MQ=255)
                                                                   tctcAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAAt                                                                   >  1:65318/1‑141 (MQ=255)
                                                                        atatCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTtctc                                                              <  2:214483/141‑1 (MQ=255)
                                                                         tatCCAGGAATTTTCTTTATAATTGTAGAACTATTTCTTATGCTGTTTAATTACTATACTAAAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCa                                                             <  2:134412/141‑1 (MQ=255)
                                                                           tCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAg                                                           <  1:214829/141‑1 (MQ=255)
                                                                           tCCAGAAATTTGCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAg                                                           <  1:242510/141‑1 (MQ=255)
                                                                                  aTTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACttt                                                    >  2:115504/1‑141 (MQ=255)
                                                                                        tttATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTaa                                              >  1:112841/1‑141 (MQ=255)
                                                                                              aTTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAAtt                                        >  2:244821/1‑141 (MQ=255)
                                                                                              aTTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGAAATTTCTCAAGAAACTTTAAGTaaacactt                                        >  2:25196/1‑136 (MQ=255)
                                                                                               ttGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTa                                       <  2:16446/141‑1 (MQ=255)
                                                                                                tGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAACCACAGAAGTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTaa                                      <  2:200652/141‑1 (MQ=255)
                                                                                                   aGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAg                                   >  2:68096/1‑141 (MQ=255)
                                                                                                      aCTATTGCTTATGCTGTATAAGTACTATACTACAAATAAAAAATATAAATATAAAAGTTAAATTAATGAAAAATAGAATTATAGAATATAAAAAAAAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAgtgt                                <  2:150771/141‑1 (MQ=255)
                                                                                                       cTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTc                               <  1:150211/141‑1 (MQ=255)
                                                                                                           ttattATACTGTTTAATTAATATAAAACAAATAAAAAATAAACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAAAAAAAAAAAAAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAgg                           <  2:202446/138‑1 (MQ=255)
                                                                                                           ttCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAgg                           >  1:167472/1‑141 (MQ=255)
                                                                                                           ttCTTATGATGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAgg                           <  1:9093/141‑1 (MQ=255)
                                                                                                            tCTTATGCTGTTTAATTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGc                          >  1:73070/1‑141 (MQ=255)
                                                                                                               tATGCTGTTTAATTACTATACTAAAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCaaa                       <  2:154546/141‑1 (MQ=255)
                                                                                                                aTGCTGTTTAATTACTATACTACAAATAAAAAAGATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAAc                      <  1:174501/141‑1 (MQ=255)
                                                                                                                          aTTACTATACTACAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCa            <  1:71210/141‑1 (MQ=255)
                                                                                                                             actatactaCAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATa         >  2:117963/1‑141 (MQ=255)
                                                                                                                               tatactaCAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGa       >  2:244429/1‑141 (MQ=255)
                                                                                                                                   ctacAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGTAATTTCTCAAGAAACTATAAGTAAAGAATTAAAAGTATCTAGGCAAACTATTAATACAATAGaaaa  >  2:218569/1‑140 (MQ=255)
                                                                                                                                   ctacAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATATCTCAAGAAACTATAAGTAAAGAAATAAAAATATCTAATAAAACTATTAATCAAAAAGaaaa  >  2:235558/1‑140 (MQ=255)
                                                                                                                                    tacAAATAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAAAAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAACa  >  2:214249/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                      
TTGTATGTTATTTACACTAGTGCTTAAATTTACAGGTTTGTCACCAAGTATTGAAGGATCTTGGTTTTCTCAATATCCAGAAATTTTCTTTATAATTGTAGCACTATTTCTTATGCTGTTTAATTACTATACTACAAATAAAAAAATATACATCTAAAGGTTAAATTAATGAAAAATAGAATTAGAGAATATAGAAAACAAAAAGGAATTTCTCAAGAAACTTTAAGTAAAGAATTAAAAGTGTCTAGGCAAACTATTAATGCAATAGAAAACA  >  CP000731/25524‑25797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: