Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 100,683 G→A 8.1% intergenic (‑185/+244) USA300HOU_0099 ← / ← USA300HOU_0101 possible MFS family major facilitator transporter/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730100,6830GA 8.1% 127.9 / 4.2 50intergenic (‑185/+244)USA300HOU_0099/USA300HOU_0101possible MFS family major facilitator transporter/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (29/17);  new base A (2/2);  total (31/19)
Fisher's exact test for biased strand distribution p-value = 6.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.10e-01

CTATAAATTGAGAGTCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATGGAGTACCAATAGAGTGGTG  >  CP000730/100544‑100822
                                                                                                                                           |                                                                                                                                           
ctATAAATTGAGAGTCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGc                                                                                                                                            >  1:421221/1‑141 (MQ=255)
  ataAATTGAGAGTCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCa                                                                                                                                          >  2:295100/1‑141 (MQ=255)
     aaTTGAGAGCCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAACCTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCt                                                                                                                                       <  1:101604/141‑1 (MQ=255)
      aTTGAGAGTCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTCTTTTGAAGTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTa                                                                                                                                      <  1:292693/141‑1 (MQ=255)
        tGAGAGTCGTTTAAAATATCGAATGGTTTCTTGCCTTCGCTGATCAACAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGATATGCGGATTGTCGCCACCTATg                                                                                                                                    >  2:299715/1‑141 (MQ=255)
        tGAGAGTCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATGTGAATTGGTTGACTAAAGGTTGTGCTTTGGGATGCGGTTTGTCGcagactatg                                                                                                                                    >  2:200775/1‑133 (MQ=255)
            agTCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTAGTTTGGGGATTGTGGCCACCTATGGTTa                                                                                                                                >  2:145844/1‑141 (MQ=255)
            agTCGTTTAAAATATCGAATGGTTTATTGACTTCGCCGATCAAAAATCTAGAGTTAGTAATATTCATAAGCTCAAATATTAATCTGAATTGGTTTACTAAAGGTGGTGCTTTGGTATGCGGATTGTCGCAACCTATGATTa                                                                                                                                >  2:430586/1‑141 (MQ=255)
                gTTTAAAATATCGAATGGTTTATTGCACTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAACGGTTGTGCTTTGGTATGCGGATTGTCGGCACCTATGATTAAAAt                                                                                                                            >  2:119530/1‑141 (MQ=255)
                  ttAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCa                                                                                                                          >  1:266346/1‑141 (MQ=255)
                                     aTTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACAt                                                                                                       <  2:271496/141‑1 (MQ=255)
                                      ttGCCTTCGCCGATCAAAAATCTATAGTTCGTAATATTCATAAACTCAAATCTTAATTTGAATTCGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCACATACTTTCTTTGTTACATg                                                                                                      >  2:66480/1‑141 (MQ=255)
                                           ttCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGTTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACTTGAtttt                                                                                                 >  2:304648/1‑140 (MQ=255)
                                              cccGATCAAAAATCTTTAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCttt                                                                                              <  2:148691/140‑1 (MQ=255)
                                                      aaaaTCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCACCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGt                                                                                      >  2:367766/1‑141 (MQ=255)
                                                      aaaaTCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCACCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGt                                                                                      >  2:137399/1‑141 (MQ=255)
                                                         aTCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTa                                                                                   >  1:350814/1‑141 (MQ=255)
                                                          tCTATAGTTAGTAATATTCATAAACTGAAATATTAATTTTAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTAt                                                                                  <  1:406791/141‑1 (MQ=255)
                                                           cTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAGTTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTTTCGCCACCTAGGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTTAAGTTGTCTAtt                                                                                 <  2:182472/141‑1 (MQ=255)
                                                                gttagtAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTTAATTTGTCTATTTGCGt                                                                            >  2:658/1‑141 (MQ=255)
                                                                  tagtAATATTCATAAACTCAAATATTAATTTGAAATGTTTGACTAAAGGTTGAGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTAt                                                                          >  1:293075/1‑141 (MQ=255)
                                                                      aaTATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTAtctcc                                                                      >  2:114186/1‑140 (MQ=255)
                                                                       atatTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTTTTACATGATTTCTTTGAAGTTGTCTATTTGCGTTTCTCGc                                                                     >  2:5309/1‑141 (MQ=255)
                                                                         atTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTTTGTTTTGTTTTCTTTCAAGTTGTCTATTTTCTTATCTTGcgg                                                                   >  2:259268/1‑139 (MQ=255)
                                                                         atTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCaa                                                                   <  1:242137/141‑1 (MQ=255)
                                                                           tCATAAACTCAAATATTAATTTGAATTTGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATTAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATg                                                                 <  2:229470/141‑1 (MQ=255)
                                                                            cATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTGAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGa                                                                >  1:336622/1‑141 (MQ=255)
                                                                            cATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGTTTTGTTTTCTTTGAAGTTGTCTATTTGCGtgtgttgctatgg                                                                >  2:354111/1‑129 (MQ=255)
                                                                            cATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGa                                                                >  1:71943/1‑141 (MQ=255)
                                                                                  cTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCTACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTCTCTCACAATGAATTGGt                                                          >  2:309548/1‑141 (MQ=255)
                                                                                  cTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGt                                                          >  2:406403/1‑141 (MQ=255)
                                                                                  cTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGt                                                          <  1:405012/141‑1 (MQ=255)
                                                                                  cTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCAACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTAGGt                                                          >  2:309539/1‑141 (MQ=255)
                                                                                    cAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTcc                                                        >  1:455195/1‑141 (MQ=255)
                                                                                          ttAAGTTGGCTTTGTTGTCTAAATGGTGTTGTTCGGTATGCTAGTTTTCGCCACCTATAATTTAAATCTAATACTTTTTTTGTCACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCTCAATATCTCTGTCCATCTAt                                                  <  2:346708/141‑1 (MQ=255)
                                                                                            aaTTTCAATTGGTTGACTAAAGGTTTTGCTTTGGTATGCAGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCa                                                <  1:33738/141‑1 (MQ=255)
                                                                                                tGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCACCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGa                                            <  1:137399/141‑1 (MQ=255)
                                                                                                tGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCACCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGa                                            <  1:367766/141‑1 (MQ=255)
                                                                                                              aaaGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTACCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGAc                              <  1:280998/141‑1 (MQ=255)
                                                                                                               aaGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGCCATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACg                             >  2:53851/1‑141 (MQ=255)
                                                                                                               aaGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACg                             >  2:192203/1‑141 (MQ=255)
                                                                                                               aaGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACg                             >  1:376261/1‑141 (MQ=255)
                                                                                                                aGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGc                            <  1:161003/141‑1 (MQ=255)
                                                                                                                 ggTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCATTGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGcc                           >  2:235001/1‑140 (MQ=255)
                                                                                                                        cTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTATCCAAAGTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATgg                    >  1:433436/1‑141 (MQ=255)
                                                                                                                                  cGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATGGAGTACCAATa          >  1:154468/1‑141 (MQ=255)
                                                                                                                                    gATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATGGAGTACCAATaga        <  1:192203/141‑1 (MQ=255)
                                                                                                                                      ttGTCGCCACCTATTATTAAAATCAAATACTTTTTTTGTGACATGATGTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATGGAGTACCAATAGAgt      <  2:304455/141‑1 (MQ=255)
                                                                                                                                      ttGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATGGAGTACCAATAGAgt      <  2:336622/141‑1 (MQ=255)
                                                                                                                                          cGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATGGAGTACCAATAGAgtggtg  <  2:350814/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                           
CTATAAATTGAGAGTCGTTTAAAATATCGAATGGTTTATTGCCTTCGCCGATCAAAAATCTATAGTTAGTAATATTCATAAACTCAAATATTAATTTGAATTGGTTGACTAAAGGTTGTGCTTTGGTATGCGGATTGTCGCCACCTATGATTAAAATCAAATACTTTTTTTGTGACATGATTTCTTTGAAGTTGTCTATTTGCGTATCTCGCAATGACTCGGTCCATCTATCAATGAAGAGTTTTAAAGACGCACTCATGGAGTACCAATAGAGTGGTG  >  CP000730/100544‑100822

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: ‑