Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,268,562 A→T 7.3% intergenic (‑450/+88) USA300HOU_2142 ← / ← USA300HOU_2143 hypothetical protein/possible HAD superfamily hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,268,5620AT 7.3% 171.6 / 6.3 55intergenic (‑450/+88)USA300HOU_2142/USA300HOU_2143hypothetical protein/possible HAD superfamily hydrolase
Reads supporting (aligned to +/- strand):  ref base A (21/30);  new base T (2/2);  total (23/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.39e-01

ACCTTAAAACAAGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTGCGCCATCCTC  >  CP000730/2268426‑2268697
                                                                                                                                         |                                                                                                                                       
aCCTTAAAACAAGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACAtt                                                                                                                                     >  1:185240/1‑141 (MQ=255)
aCCTTAAAACAAGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACAtt                                                                                                                                     >  1:214945/1‑141 (MQ=255)
      aaaCAAGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTaa                                                                                                                               <  1:540476/141‑1 (MQ=255)
      aaaCAAGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTaa                                                                                                                               <  1:540593/141‑1 (MQ=255)
       aaCAAGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGCGTTTGTCCAATTACATCTAGATGATTCAACTATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAAt                                                                                                                              <  1:78438/141‑1 (MQ=255)
         cAAGAAATATTATTCANAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAg                                                                                                                            >  1:433344/1‑141 (MQ=255)
          aaGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGa                                                                                                                           <  1:539667/141‑1 (MQ=255)
          aaGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAAAAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGa                                                                                                                           <  1:468670/141‑1 (MQ=255)
            gAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGa                                                                                                                                         >  1:42360/1‑125 (MQ=255)
            gAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGa                                                                                                                                         <  2:42360/125‑1 (MQ=255)
                tattatTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAAGTTATTTTCTATTAGAAAAtg                                                                                                                      >  1:5080/1‑140 (MQ=39)
                  ttattCAAAATCAATGAATTTCGTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACt                                                                                                                   <  2:427650/141‑1 (MQ=255)
                        aaaaTCAATGAATTTCCTATCTTATTAG‑‑TTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAAGTTATTTTCTATTAGAAAAtgtcttactgct                                                                                                            <  2:225651/141‑12 (MQ=25)
                          aaTCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAAGTTATTTTCTATTAGAAAAtgtcttactgct                                                                                                            <  1:568568/141‑12 (MQ=37)
                           aTCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGctc                                                                                                          <  2:206829/141‑1 (MQ=255)
                             cAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCtt                                                                                                        <  1:376043/141‑1 (MQ=255)
                             cAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCtt                                                                                                        <  2:409266/141‑1 (MQ=255)
                              aaTGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCttt                                                                                                       >  1:155553/1‑141 (MQ=255)
                               aTGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTg                                                                                                      >  1:429684/1‑141 (MQ=255)
                                 gAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTa                                                                                                    >  2:560948/1‑141 (MQ=255)
                                   aTTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACa                                                                                                  <  2:508632/141‑1 (MQ=255)
                                      tCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTa                                                                                               <  2:9803/141‑1 (MQ=255)
                                       ccTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTTATAGAAAATAACTTTACTGCTCTTTGTTCATTAc                                                                                              >  2:117299/1‑141 (MQ=255)
                                         tATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACtc                                                                                            <  2:439368/141‑1 (MQ=255)
                                            cTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACtcatc                                                                                         <  1:329794/141‑1 (MQ=255)
                                             ttattaGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACtcatca                                                                                        <  2:423608/141‑1 (MQ=255)
                                                ttaGTTTTAACAATAGTTATTCTCATAGAGCTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACt                                                                                     >  2:776905/1‑141 (MQ=255)
                                                 taGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTa                                                                                    >  2:311468/1‑141 (MQ=255)
                                                    ttttAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTg                                                                                 <  2:462699/141‑1 (MQ=255)
                                                       tAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGtaa                                                                              <  1:358497/141‑1 (MQ=255)
                                                       tAACAACATTTAGTCTAATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGtaa                                                                              <  1:326653/141‑1 (MQ=255)
                                                             tatttattCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGtaaattaaa                                                                        >  1:392870/1‑141 (MQ=255)
                                                              atttattCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGtaaattaaat                                                                       <  2:691108/141‑1 (MQ=255)
                                                                  attCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATtaaataata                                                                   <  2:582525/141‑1 (MQ=255)
                                                                   ttCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATtaaataataa                                                                  >  1:261526/1‑141 (MQ=255)
                                                                    tctcATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATtaaataataaa                                                                 <  2:761954/141‑1 (MQ=255)
                                                                      tcATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATtaaataataaata                                                               >  1:273861/1‑141 (MQ=255)
                                                                        aTAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAAc                                                             <  1:344046/141‑1 (MQ=255)
                                                                         tAGAGTTTGTCCACTTAAATATAGATGATTCAAATATATATAAGCACACAAAAGAGCAGTAAGACATTTTCTAATAAAAAATAACTTTACCGCTCTTTGTACATTCTGCAGCAGCTATGGTAAATTAAATAATAAATAACt                                                            >  2:13130/1‑141 (MQ=255)
                                                                         tAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACt                                                            >  2:424685/1‑141 (MQ=255)
                                                                             gTTTGTCCAATTAAATATAGATGATTAAAATAATAATAAAAAAAAAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCt                                                        <  2:354426/141‑1 (MQ=255)
                                                                               ttGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTAt                                                      >  1:620458/1‑141 (MQ=255)
                                                                                  tCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTAtttt                                                   >  2:107796/1‑141 (MQ=255)
                                                                                  tCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTAtttt                                                   <  2:484539/141‑1 (MQ=255)
                                                                                            tataGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGc                                         <  1:288844/141‑1 (MQ=255)
                                                                                              taGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTa                                       <  2:157320/141‑1 (MQ=255)
                                                                                                           tatTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGc                          <  1:757402/141‑1 (MQ=255)
                                                                                                                 taAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAata                    >  1:27908/1‑141 (MQ=255)
                                                                                                                 taAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAata                    >  2:263706/1‑141 (MQ=255)
                                                                                                                         acaaaGAGCAGTAAAGTTATTTTCTATTAGAAAATGTCTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTtgctg            >  1:594640/3‑141 (MQ=25)
                                                                                                                            aaGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTTCCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTgcgc         <  2:392364/141‑1 (MQ=255)
                                                                                                                             agagCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTGCGcc        >  2:87193/1‑141 (MQ=255)
                                                                                                                               agCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTCAATATGTTGCTGCGCCAt      >  1:241856/1‑141 (MQ=255)
                                                                                                                                 ccgTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTGCGCCATcc    <  1:559072/139‑1 (MQ=255)
                                                                                                                                 cAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAGCCGCCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTGCGCCATcc    <  1:280311/141‑1 (MQ=255)
                                                                                                                                 cAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTGCGCCATcc    <  2:684422/141‑1 (MQ=255)
                                                                                                                                   gTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTGCGCCATCctc  >  2:430182/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                       
ACCTTAAAACAAGAAATATTATTCAAAATCAATGAATTTCCTATCTTATTAGTTTTAACAATATTTATTCTCATAGAGTTTGTCCAATTAAATATAGATGATTCAAATATTTATAAGCATACAAAAGAGCAGTAAGACATTTTCTAATAGAAAATAACTTTACTGCTCTTTGTACATTACTCATCAACTATTGTAAATTAAATAATAAATAACTACCTATTTTATTATTCAGCTAAAAAATGCTCTGCTAAATATTTTGCTGCGCCATCCTC  >  CP000730/2268426‑2268697

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